Starting phenix.real_space_refine on Tue Aug 4 12:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypq_34011/08_2026/7ypq_34011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypq_34011/08_2026/7ypq_34011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ypq_34011/08_2026/7ypq_34011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypq_34011/08_2026/7ypq_34011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ypq_34011/08_2026/7ypq_34011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypq_34011/08_2026/7ypq_34011.map" } resolution = 3.1 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= 0.002 sd= 0.137 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 12 5.16 5 C 1811 2.51 5 N 493 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2915 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "Q" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 0.61, per 1000 atoms: 0.21 Number of scatterers: 2915 At special positions: 0 Unit cell: (65.55, 79.8, 75.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 11 15.00 O 588 8.00 N 493 7.00 C 1811 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: 0.22 Conformation dependent library (CDL) restraints added in 92.0 milliseconds 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 634 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 4 sheets defined 18.7% alpha, 48.6% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.742A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 336 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 66 removed outlier: 6.671A pdb=" N LYS A 75 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 61 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 73 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR A 63 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR A 71 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 65 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 72 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 12.776A pdb=" N LEU A 112 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A 84 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE A 114 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 86 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 116 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 108 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 114 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN A 106 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 116 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.221A pdb=" N LEU A 236 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU A 184 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 238 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 186 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 240 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N SER A 239 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N CYS A 226 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ASN A 241 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 224 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 217 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 144 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 14.863A pdb=" N LEU A 146 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 13.885A pdb=" N GLU A 172 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 148 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU A 170 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N PHE A 150 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 168 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 152 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 4.579A pdb=" N VAL A 348 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 347 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 369 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP A 349 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 367 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 351 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 288 102 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 0.33 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 919 1.34 - 1.46: 637 1.46 - 1.57: 1394 1.57 - 1.69: 21 1.69 - 1.81: 19 Bond restraints: 2990 Sorted by residual: bond pdb=" C3' DA Q 4 " pdb=" O3' DA Q 4 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.37e+00 bond pdb=" C3' DA Q 5 " pdb=" O3' DA Q 5 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" C LEU A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.330 1.302 0.028 1.26e-02 6.30e+03 4.94e+00 bond pdb=" C3' DA Q 1 " pdb=" C2' DA Q 1 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.48e+00 bond pdb=" O4' DA Q 5 " pdb=" C1' DA Q 5 " ideal model delta sigma weight residual 1.420 1.397 0.023 1.10e-02 8.26e+03 4.46e+00 ... (remaining 2985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 3869 1.32 - 2.65: 179 2.65 - 3.97: 26 3.97 - 5.29: 5 5.29 - 6.62: 2 Bond angle restraints: 4081 Sorted by residual: angle pdb=" O4' DA Q 1 " pdb=" C4' DA Q 1 " pdb=" C3' DA Q 1 " ideal model delta sigma weight residual 106.00 104.48 1.52 6.00e-01 2.78e+00 6.44e+00 angle pdb=" O4' DA Q 2 " pdb=" C4' DA Q 2 " pdb=" C3' DA Q 2 " ideal model delta sigma weight residual 106.00 104.50 1.50 6.00e-01 2.78e+00 6.26e+00 angle pdb=" CA GLU A 216 " pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " ideal model delta sigma weight residual 114.10 119.08 -4.98 2.00e+00 2.50e-01 6.21e+00 angle pdb=" O5' DA Q 5 " pdb=" C5' DA Q 5 " pdb=" C4' DA Q 5 " ideal model delta sigma weight residual 109.40 111.37 -1.97 8.00e-01 1.56e+00 6.07e+00 angle pdb=" O4' DA Q 7 " pdb=" C4' DA Q 7 " pdb=" C3' DA Q 7 " ideal model delta sigma weight residual 106.00 107.36 -1.36 6.00e-01 2.78e+00 5.11e+00 ... (remaining 4076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1553 17.98 - 35.96: 180 35.96 - 53.94: 56 53.94 - 71.92: 12 71.92 - 89.90: 4 Dihedral angle restraints: 1805 sinusoidal: 823 harmonic: 982 Sorted by residual: dihedral pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N LEU A 352 " pdb=" CA LEU A 352 " ideal model delta harmonic sigma weight residual -180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 219 " pdb=" C PHE A 219 " pdb=" N ASN A 220 " pdb=" CA ASN A 220 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N LYS A 305 " pdb=" CA LYS A 305 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 267 0.035 - 0.070: 130 0.070 - 0.104: 38 0.104 - 0.139: 22 0.139 - 0.174: 2 Chirality restraints: 459 Sorted by residual: chirality pdb=" C3' DA Q 5 " pdb=" C4' DA Q 5 " pdb=" O3' DA Q 5 " pdb=" C2' DA Q 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA ILE A 310 " pdb=" N ILE A 310 " pdb=" C ILE A 310 " pdb=" CB ILE A 310 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 456 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 377 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 378 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 216 " 0.004 2.00e-02 2.50e+03 7.45e-03 5.55e-01 pdb=" C GLU A 216 " -0.013 2.00e-02 2.50e+03 pdb=" O GLU A 216 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS A 217 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.004 2.00e-02 2.50e+03 7.39e-03 5.46e-01 pdb=" C ILE A 297 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.005 2.00e-02 2.50e+03 pdb=" N SER A 298 " 0.004 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 611 2.79 - 3.32: 2563 3.32 - 3.84: 4682 3.84 - 4.37: 5819 4.37 - 4.90: 9706 Nonbonded interactions: 23381 Sorted by model distance: nonbonded pdb=" O CYS A 210 " pdb=" OG SER A 214 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 98 " pdb=" NE2 GLN A 243 " model vdw 2.360 3.120 nonbonded pdb=" OG SER A 292 " pdb=" OP1 DA Q 9 " model vdw 2.402 3.040 nonbonded pdb=" NH2 ARG A 223 " pdb=" O ASN A 241 " model vdw 2.413 3.120 nonbonded pdb=" O ASN A 358 " pdb=" OD1 ASN A 358 " model vdw 2.421 3.040 ... (remaining 23376 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.880 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.005 0.041 2990 Z= 0.300 Angle : 0.651 6.618 4081 Z= 0.404 Chirality : 0.048 0.174 459 Planarity : 0.002 0.029 481 Dihedral : 17.794 89.903 1171 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.46), residues: 323 helix: 0.04 (0.66), residues: 62 sheet: -0.22 (0.45), residues: 125 loop : -0.73 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 294 TYR 0.010 0.001 TYR A 299 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.30 ( 2990) covalent geometry : angle 0.65121 / 0.40 ( 4081) hydrogen bonds : bond 0.12357 / 6.63 ( 102) hydrogen bonds : angle 7.17021 / 4.77 ( 291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.104 Fit side-chains REVERT: A 80 ASN cc_start: 0.8098 (m110) cc_final: 0.7333 (t0) REVERT: A 130 CYS cc_start: 0.8140 (m) cc_final: 0.7935 (m) REVERT: A 206 ASP cc_start: 0.7749 (m-30) cc_final: 0.7522 (m-30) REVERT: A 262 TYR cc_start: 0.8966 (p90) cc_final: 0.8652 (p90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0678 time to fit residues: 4.5150 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121928 restraints weight = 2967.750| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.13 r_work: 0.3112 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2990 Z= 0.172 Angle : 0.592 7.850 4081 Z= 0.330 Chirality : 0.044 0.132 459 Planarity : 0.003 0.022 481 Dihedral : 16.853 71.091 510 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.97 % Allowed : 3.87 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.46), residues: 323 helix: 0.69 (0.69), residues: 62 sheet: -0.11 (0.45), residues: 125 loop : -0.67 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.010 0.001 TYR A 351 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 2990) covalent geometry : angle 0.59180 / 0.33 ( 4081) hydrogen bonds : bond 0.04124 / 2.33 ( 102) hydrogen bonds : angle 5.90341 / 3.95 ( 291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.062 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8263 (m110) cc_final: 0.7429 (t0) REVERT: A 130 CYS cc_start: 0.8396 (m) cc_final: 0.8030 (m) REVERT: A 213 LYS cc_start: 0.8485 (mttm) cc_final: 0.8015 (mptt) REVERT: A 262 TYR cc_start: 0.9023 (p90) cc_final: 0.8634 (p90) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.0426 time to fit residues: 2.3519 Evaluate side-chains 43 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.167549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120942 restraints weight = 2973.124| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.15 r_work: 0.3100 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2990 Z= 0.175 Angle : 0.563 6.567 4081 Z= 0.318 Chirality : 0.044 0.139 459 Planarity : 0.002 0.022 481 Dihedral : 16.898 72.256 510 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.97 % Allowed : 6.45 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.47), residues: 323 helix: 0.93 (0.70), residues: 62 sheet: 0.03 (0.46), residues: 120 loop : -0.55 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.012 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 2990) covalent geometry : angle 0.56290 / 0.32 ( 4081) hydrogen bonds : bond 0.03594 / 2.10 ( 102) hydrogen bonds : angle 5.53674 / 3.69 ( 291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8291 (m110) cc_final: 0.7432 (t0) REVERT: A 130 CYS cc_start: 0.8371 (m) cc_final: 0.8012 (m) REVERT: A 213 LYS cc_start: 0.8428 (mttm) cc_final: 0.7869 (mptt) REVERT: A 262 TYR cc_start: 0.9032 (p90) cc_final: 0.8621 (p90) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.0695 time to fit residues: 4.0412 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.168839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122206 restraints weight = 2948.010| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.16 r_work: 0.3133 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2990 Z= 0.162 Angle : 0.544 5.556 4081 Z= 0.307 Chirality : 0.044 0.137 459 Planarity : 0.002 0.022 481 Dihedral : 17.242 73.957 510 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.61 % Allowed : 9.35 % Favored : 89.03 % 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 are not related in a simple way. whole: -0.03 (0.47), residues: 323 helix: 1.08 (0.69), residues: 62 sheet: 0.10 (0.46), residues: 120 loop : -0.51 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.009 0.001 TYR A 351 PHE 0.008 0.001 PHE A 258 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 2990) covalent geometry : angle 0.54361 / 0.31 ( 4081) hydrogen bonds : bond 0.03340 / 1.99 ( 102) hydrogen bonds : angle 5.26698 / 3.52 ( 291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8260 (m110) cc_final: 0.7445 (t0) REVERT: A 130 CYS cc_start: 0.8344 (m) cc_final: 0.8020 (m) REVERT: A 213 LYS cc_start: 0.8460 (mttm) cc_final: 0.7942 (mptt) REVERT: A 262 TYR cc_start: 0.9018 (p90) cc_final: 0.8597 (p90) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.0728 time to fit residues: 4.1488 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.168245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120636 restraints weight = 2909.852| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.20 r_work: 0.3093 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2990 Z= 0.184 Angle : 0.547 5.366 4081 Z= 0.306 Chirality : 0.044 0.138 459 Planarity : 0.002 0.022 481 Dihedral : 17.704 75.075 510 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.94 % Allowed : 9.03 % Favored : 89.03 % 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 are not related in a simple way. whole: -0.00 (0.47), residues: 323 helix: 1.15 (0.70), residues: 62 sheet: 0.14 (0.46), residues: 120 loop : -0.55 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.019 0.001 TYR A 260 PHE 0.009 0.001 PHE A 189 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 2990) covalent geometry : angle 0.54691 / 0.31 ( 4081) hydrogen bonds : bond 0.03314 / 1.99 ( 102) hydrogen bonds : angle 5.22511 / 3.50 ( 291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8157 (m110) cc_final: 0.7325 (t0) REVERT: A 130 CYS cc_start: 0.8384 (m) cc_final: 0.8039 (m) REVERT: A 213 LYS cc_start: 0.8451 (mttm) cc_final: 0.7928 (mptt) REVERT: A 257 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7714 (mm-30) REVERT: A 262 TYR cc_start: 0.9021 (p90) cc_final: 0.8610 (p90) outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.0742 time to fit residues: 4.0404 Evaluate side-chains 47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.169084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122013 restraints weight = 2909.431| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.18 r_work: 0.3117 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2990 Z= 0.143 Angle : 0.508 4.943 4081 Z= 0.287 Chirality : 0.042 0.135 459 Planarity : 0.002 0.020 481 Dihedral : 17.671 76.746 510 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.26 % Allowed : 9.03 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.47), residues: 323 helix: 1.26 (0.71), residues: 62 sheet: 0.16 (0.46), residues: 120 loop : -0.54 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.014 0.001 TYR A 260 PHE 0.007 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 2990) covalent geometry : angle 0.50772 / 0.29 ( 4081) hydrogen bonds : bond 0.03096 / 1.86 ( 102) hydrogen bonds : angle 5.08777 / 3.41 ( 291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.130 Fit side-chains REVERT: A 80 ASN cc_start: 0.8157 (m110) cc_final: 0.7342 (t0) REVERT: A 99 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6310 (mmmt) REVERT: A 130 CYS cc_start: 0.8364 (m) cc_final: 0.8039 (m) REVERT: A 213 LYS cc_start: 0.8470 (mttm) cc_final: 0.7959 (mptt) REVERT: A 257 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 262 TYR cc_start: 0.9011 (p90) cc_final: 0.8582 (p90) outliers start: 7 outliers final: 7 residues processed: 49 average time/residue: 0.0726 time to fit residues: 4.3370 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.167319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.120552 restraints weight = 2973.786| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.17 r_work: 0.3111 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2990 Z= 0.188 Angle : 0.542 5.201 4081 Z= 0.304 Chirality : 0.044 0.141 459 Planarity : 0.002 0.021 481 Dihedral : 17.680 77.771 510 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.94 % Allowed : 10.97 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.47), residues: 323 helix: 1.23 (0.71), residues: 62 sheet: 0.19 (0.47), residues: 120 loop : -0.54 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.013 0.001 TYR A 260 PHE 0.009 0.001 PHE A 189 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 2990) covalent geometry : angle 0.54214 / 0.30 ( 4081) hydrogen bonds : bond 0.03224 / 1.94 ( 102) hydrogen bonds : angle 5.09337 / 3.42 ( 291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8183 (m110) cc_final: 0.7346 (t0) REVERT: A 113 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 130 CYS cc_start: 0.8382 (m) cc_final: 0.8044 (m) REVERT: A 213 LYS cc_start: 0.8489 (mttm) cc_final: 0.7995 (mptt) REVERT: A 257 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 262 TYR cc_start: 0.9026 (p90) cc_final: 0.8607 (p90) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0723 time to fit residues: 4.1040 Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.168141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121402 restraints weight = 2976.136| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.18 r_work: 0.3109 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2990 Z= 0.151 Angle : 0.527 7.085 4081 Z= 0.293 Chirality : 0.043 0.135 459 Planarity : 0.002 0.020 481 Dihedral : 17.648 79.027 510 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.58 % Allowed : 10.97 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.47), residues: 323 helix: 1.30 (0.71), residues: 62 sheet: 0.19 (0.46), residues: 120 loop : -0.53 (0.52), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.011 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 2990) covalent geometry : angle 0.52744 / 0.29 ( 4081) hydrogen bonds : bond 0.03063 / 1.84 ( 102) hydrogen bonds : angle 5.02797 / 3.37 ( 291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.106 Fit side-chains REVERT: A 80 ASN cc_start: 0.8169 (m110) cc_final: 0.7343 (t0) REVERT: A 99 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6373 (mmmt) REVERT: A 113 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7235 (mp) REVERT: A 130 CYS cc_start: 0.8361 (m) cc_final: 0.8024 (m) REVERT: A 213 LYS cc_start: 0.8477 (mttm) cc_final: 0.7985 (mptt) REVERT: A 257 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 262 TYR cc_start: 0.9019 (p90) cc_final: 0.8591 (p90) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.0720 time to fit residues: 4.1813 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.167278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119494 restraints weight = 2995.825| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.24 r_work: 0.3088 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2990 Z= 0.202 Angle : 0.561 7.438 4081 Z= 0.309 Chirality : 0.044 0.142 459 Planarity : 0.003 0.022 481 Dihedral : 17.678 80.106 510 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.58 % Allowed : 11.61 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.47), residues: 323 helix: 1.21 (0.71), residues: 62 sheet: 0.26 (0.47), residues: 118 loop : -0.62 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.012 0.001 TYR A 260 PHE 0.009 0.001 PHE A 189 HIS 0.001 0.000 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 ( 2990) covalent geometry : angle 0.56125 / 0.31 ( 4081) hydrogen bonds : bond 0.03231 / 1.95 ( 102) hydrogen bonds : angle 5.08048 / 3.41 ( 291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.108 Fit side-chains REVERT: A 80 ASN cc_start: 0.8197 (m110) cc_final: 0.7344 (t0) REVERT: A 99 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6383 (mmmt) REVERT: A 113 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 130 CYS cc_start: 0.8402 (m) cc_final: 0.8054 (m) REVERT: A 213 LYS cc_start: 0.8494 (mttm) cc_final: 0.8009 (mptt) REVERT: A 257 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 262 TYR cc_start: 0.9032 (p90) cc_final: 0.8609 (p90) REVERT: A 305 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8395 (mmmt) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.0691 time to fit residues: 4.3079 Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.168249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120788 restraints weight = 2964.132| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.22 r_work: 0.3109 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2990 Z= 0.160 Angle : 0.563 10.072 4081 Z= 0.306 Chirality : 0.043 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.650 81.161 510 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 12.90 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.47), residues: 323 helix: 1.28 (0.71), residues: 62 sheet: 0.28 (0.47), residues: 118 loop : -0.62 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.011 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 2990) covalent geometry : angle 0.56299 / 0.31 ( 4081) hydrogen bonds : bond 0.03106 / 1.87 ( 102) hydrogen bonds : angle 5.02092 / 3.37 ( 291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.109 Fit side-chains REVERT: A 80 ASN cc_start: 0.8183 (m110) cc_final: 0.7337 (t0) REVERT: A 99 LYS cc_start: 0.6977 (mmtt) cc_final: 0.6357 (mmmt) REVERT: A 113 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7299 (mp) REVERT: A 130 CYS cc_start: 0.8380 (m) cc_final: 0.8026 (m) REVERT: A 213 LYS cc_start: 0.8471 (mttm) cc_final: 0.7985 (mptt) REVERT: A 257 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 262 TYR cc_start: 0.9022 (p90) cc_final: 0.8602 (p90) REVERT: A 305 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8382 (mmmt) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.0707 time to fit residues: 4.1625 Evaluate side-chains 50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.0050 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.168548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121242 restraints weight = 2949.597| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.21 r_work: 0.3106 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2990 Z= 0.148 Angle : 0.550 9.678 4081 Z= 0.302 Chirality : 0.043 0.136 459 Planarity : 0.002 0.023 481 Dihedral : 17.644 81.660 510 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 13.55 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.47), residues: 323 helix: 1.29 (0.71), residues: 62 sheet: 0.28 (0.47), residues: 118 loop : -0.61 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.011 0.001 TYR A 260 PHE 0.008 0.001 PHE A 189 HIS 0.001 0.000 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 2990) covalent geometry : angle 0.54978 / 0.30 ( 4081) hydrogen bonds : bond 0.03050 / 1.84 ( 102) hydrogen bonds : angle 4.99363 / 3.35 ( 291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 901.41 seconds wall clock time: 16 minutes 10.46 seconds (970.46 seconds total)