Starting phenix.real_space_refine on Fri Aug 22 15:45:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p79_17522/08_2025/8p79_17522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p79_17522/08_2025/8p79_17522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p79_17522/08_2025/8p79_17522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p79_17522/08_2025/8p79_17522.map" model { file = "/net/cci-nas-00/data/ceres_data/8p79_17522/08_2025/8p79_17522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p79_17522/08_2025/8p79_17522.cif" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3269 2.51 5 N 864 2.21 5 O 1092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5256 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "I" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "J" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Time building chain proxies: 1.21, per 1000 atoms: 0.23 Number of scatterers: 5256 At special positions: 0 Unit cell: (85.5, 93.3375, 68.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1092 8.00 N 864 7.00 C 3269 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: 0.37 Conformation dependent library (CDL) restraints added in 159.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.567A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 Processing helix chain 'H' and resid 288 through 302 removed outlier: 3.958A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 Processing helix chain 'I' and resid 49 through 71 Processing helix chain 'I' and resid 76 through 91 Processing helix chain 'I' and resid 100 through 116 removed outlier: 3.817A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS I 114 " --> pdb=" O PHE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 132 through 154 removed outlier: 4.690A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 183 through 186 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.833A pdb=" N THR I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 207 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 removed outlier: 4.227A pdb=" N LEU I 232 " --> pdb=" O MET I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 261 Processing helix chain 'I' and resid 266 through 284 removed outlier: 3.736A pdb=" N ALA I 283 " --> pdb=" O ARG I 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 68 removed outlier: 3.942A pdb=" N GLU J 68 " --> pdb=" O LYS J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.605A pdb=" N ALA J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 239 through 243 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 292 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.675A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing sheet with id=AA1, first strand: chain 'J' and resid 16 through 20 removed outlier: 5.554A pdb=" N PHE J 17 " --> pdb=" O LYS J 28 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS J 28 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134 272 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 824 1.31 - 1.44: 1380 1.44 - 1.57: 2944 1.57 - 1.71: 0 1.71 - 1.84: 49 Bond restraints: 5197 Sorted by residual: bond pdb=" CA SER I 210 " pdb=" CB SER I 210 " ideal model delta sigma weight residual 1.529 1.452 0.077 1.55e-02 4.16e+03 2.44e+01 bond pdb=" C PRO I 209 " pdb=" O PRO I 209 " ideal model delta sigma weight residual 1.237 1.177 0.061 1.26e-02 6.30e+03 2.31e+01 bond pdb=" C MET J 120 " pdb=" O MET J 120 " ideal model delta sigma weight residual 1.236 1.284 -0.048 1.15e-02 7.56e+03 1.73e+01 bond pdb=" C LEU J 143 " pdb=" O LEU J 143 " ideal model delta sigma weight residual 1.232 1.281 -0.049 1.20e-02 6.94e+03 1.66e+01 bond pdb=" CA SER I 5 " pdb=" CB SER I 5 " ideal model delta sigma weight residual 1.529 1.462 0.067 1.66e-02 3.63e+03 1.64e+01 ... (remaining 5192 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4395 1.47 - 2.95: 1971 2.95 - 4.42: 568 4.42 - 5.89: 92 5.89 - 7.37: 7 Bond angle restraints: 7033 Sorted by residual: angle pdb=" C GLU I 168 " pdb=" N GLY I 169 " pdb=" CA GLY I 169 " ideal model delta sigma weight residual 119.98 126.46 -6.48 1.11e+00 8.12e-01 3.41e+01 angle pdb=" CA ILE I 104 " pdb=" C ILE I 104 " pdb=" O ILE I 104 " ideal model delta sigma weight residual 120.95 115.86 5.09 1.04e+00 9.25e-01 2.40e+01 angle pdb=" C GLN J 221 " pdb=" N LEU J 222 " pdb=" CA LEU J 222 " ideal model delta sigma weight residual 120.28 126.80 -6.52 1.34e+00 5.57e-01 2.37e+01 angle pdb=" CA TYR I 164 " pdb=" C TYR I 164 " pdb=" O TYR I 164 " ideal model delta sigma weight residual 120.70 115.75 4.95 1.03e+00 9.43e-01 2.31e+01 angle pdb=" C LYS J 115 " pdb=" N ALA J 116 " pdb=" CA ALA J 116 " ideal model delta sigma weight residual 120.44 126.62 -6.18 1.30e+00 5.92e-01 2.26e+01 ... (remaining 7028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 2759 14.68 - 29.36: 271 29.36 - 44.03: 79 44.03 - 58.71: 29 58.71 - 73.39: 9 Dihedral angle restraints: 3147 sinusoidal: 1300 harmonic: 1847 Sorted by residual: dihedral pdb=" CA LEU J 243 " pdb=" C LEU J 243 " pdb=" N PRO J 244 " pdb=" CA PRO J 244 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ARG I 9 " pdb=" C ARG I 9 " pdb=" N HIS I 10 " pdb=" CA HIS I 10 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA THR J 175 " pdb=" C THR J 175 " pdb=" N ARG J 176 " pdb=" CA ARG J 176 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 3144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 308 0.048 - 0.095: 270 0.095 - 0.143: 141 0.143 - 0.191: 46 0.191 - 0.238: 10 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA VAL H 260 " pdb=" N VAL H 260 " pdb=" C VAL H 260 " pdb=" CB VAL H 260 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE J 75 " pdb=" CA ILE J 75 " pdb=" CG1 ILE J 75 " pdb=" CG2 ILE J 75 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LEU J 134 " pdb=" N LEU J 134 " pdb=" C LEU J 134 " pdb=" CB LEU J 134 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 772 not shown) Planarity restraints: 901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 2 " 0.033 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR I 2 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR I 2 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR I 2 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR I 2 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR I 2 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I 2 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 86 " 0.029 2.00e-02 2.50e+03 2.23e-02 9.92e+00 pdb=" CG TYR I 86 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR I 86 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR I 86 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR I 86 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR I 86 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 86 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR I 86 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 85 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C MET I 85 " -0.050 2.00e-02 2.50e+03 pdb=" O MET I 85 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR I 86 " 0.017 2.00e-02 2.50e+03 ... (remaining 898 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 732 2.78 - 3.31: 5581 3.31 - 3.84: 9407 3.84 - 4.37: 12151 4.37 - 4.90: 19035 Nonbonded interactions: 46906 Sorted by model distance: nonbonded pdb=" O GLN J 236 " pdb=" O HOH J 401 " model vdw 2.251 3.040 nonbonded pdb=" O GLU I 145 " pdb=" O HOH I 401 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR J 178 " pdb=" OE1 GLU J 205 " model vdw 2.335 3.040 nonbonded pdb=" NH1 ARG J 57 " pdb=" O HOH J 402 " model vdw 2.345 3.120 nonbonded pdb=" O ILE I 198 " pdb=" OG1 THR I 201 " model vdw 2.380 3.040 ... (remaining 46901 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.590 Find NCS groups from input model: 0.020 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.014 0.077 5197 Z= 1.003 Angle : 1.732 7.369 7033 Z= 1.301 Chirality : 0.083 0.238 775 Planarity : 0.007 0.029 901 Dihedral : 14.303 73.391 1951 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.90 % Allowed : 6.32 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.29), residues: 618 helix: -1.14 (0.22), residues: 348 sheet: 0.87 (1.26), residues: 14 loop : -0.61 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 89 TYR 0.057 0.007 TYR I 2 PHE 0.030 0.006 PHE J 295 TRP 0.032 0.007 TRP I 11 HIS 0.016 0.004 HIS I 3 Details of bonding type rmsd covalent geometry : bond 0.01350 ( 5197) covalent geometry : angle 1.73217 ( 7033) hydrogen bonds : bond 0.18133 ( 272) hydrogen bonds : angle 7.26168 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.220 Fit side-chains REVERT: H 268 ARG cc_start: 0.7166 (mtm110) cc_final: 0.6782 (mtp180) REVERT: H 281 GLN cc_start: 0.7302 (pt0) cc_final: 0.7026 (tt0) REVERT: H 306 TRP cc_start: 0.7636 (t60) cc_final: 0.7436 (t60) REVERT: I 17 GLU cc_start: 0.6530 (mp0) cc_final: 0.6105 (mp0) REVERT: I 18 GLN cc_start: 0.7347 (tt0) cc_final: 0.7095 (tt0) REVERT: I 29 LYS cc_start: 0.6977 (mtpt) cc_final: 0.5979 (pptt) REVERT: I 61 GLU cc_start: 0.7353 (tt0) cc_final: 0.7145 (tt0) REVERT: I 62 LYS cc_start: 0.7722 (mtpp) cc_final: 0.7422 (mmtt) REVERT: I 77 ARG cc_start: 0.6737 (mmp80) cc_final: 0.6197 (ptt180) REVERT: I 138 LYS cc_start: 0.7095 (tttp) cc_final: 0.6850 (ttpp) REVERT: I 189 LYS cc_start: 0.7530 (tttm) cc_final: 0.7294 (tttp) REVERT: I 197 ARG cc_start: 0.7301 (mtp85) cc_final: 0.6702 (mtt90) REVERT: I 223 ARG cc_start: 0.6570 (ttt-90) cc_final: 0.6232 (mmt90) REVERT: I 234 GLU cc_start: 0.6582 (pt0) cc_final: 0.6299 (mm-30) REVERT: I 247 GLN cc_start: 0.6646 (mt0) cc_final: 0.6444 (mt0) REVERT: I 279 ARG cc_start: 0.6179 (mtm-85) cc_final: 0.5881 (ttp-110) REVERT: J 41 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7398 (ttmm) REVERT: J 219 LEU cc_start: 0.6090 (mm) cc_final: 0.5837 (tp) REVERT: J 298 ARG cc_start: 0.6836 (mpp-170) cc_final: 0.6481 (mtt90) outliers start: 5 outliers final: 1 residues processed: 133 average time/residue: 0.6841 time to fit residues: 93.7059 Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 294 HIS H 298 GLN ** J 129 HIS ** 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 = 0.4347 r_free = 0.4347 target = 0.206484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177914 restraints weight = 2923.076| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 0.66 r_work: 0.3901 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3609 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5197 Z= 0.125 Angle : 0.561 5.539 7033 Z= 0.296 Chirality : 0.040 0.140 775 Planarity : 0.004 0.036 901 Dihedral : 4.885 52.565 690 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 9.03 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.33), residues: 618 helix: 1.70 (0.27), residues: 339 sheet: 1.29 (1.16), residues: 15 loop : 0.20 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 63 TYR 0.020 0.002 TYR I 207 PHE 0.017 0.002 PHE J 295 TRP 0.009 0.001 TRP I 11 HIS 0.005 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5197) covalent geometry : angle 0.56067 ( 7033) hydrogen bonds : bond 0.05006 ( 272) hydrogen bonds : angle 4.84654 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.209 Fit side-chains REVERT: I 29 LYS cc_start: 0.6919 (mtpt) cc_final: 0.6352 (pttp) REVERT: I 61 GLU cc_start: 0.7746 (tt0) cc_final: 0.7329 (mt-10) REVERT: I 189 LYS cc_start: 0.7736 (tttm) cc_final: 0.7524 (tptp) REVERT: I 197 ARG cc_start: 0.7534 (mtp85) cc_final: 0.7135 (mtt90) REVERT: J 120 MET cc_start: 0.8366 (mtm) cc_final: 0.8122 (mtm) REVERT: J 147 GLU cc_start: 0.7197 (pm20) cc_final: 0.6857 (pt0) outliers start: 5 outliers final: 1 residues processed: 120 average time/residue: 0.6726 time to fit residues: 83.2991 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN ** J 129 HIS ** 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 = 0.4312 r_free = 0.4312 target = 0.202396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.173165 restraints weight = 2921.127| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 0.66 r_work: 0.3866 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3561 rms_B_bonded: 4.74 restraints_weight: 0.1250 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5197 Z= 0.145 Angle : 0.577 5.431 7033 Z= 0.305 Chirality : 0.041 0.138 775 Planarity : 0.004 0.038 901 Dihedral : 4.874 53.317 690 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.90 % Allowed : 10.11 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.33), residues: 618 helix: 1.82 (0.28), residues: 345 sheet: -0.11 (1.07), residues: 20 loop : 0.41 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 63 TYR 0.018 0.002 TYR I 91 PHE 0.018 0.002 PHE I 30 TRP 0.011 0.002 TRP I 11 HIS 0.006 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5197) covalent geometry : angle 0.57689 ( 7033) hydrogen bonds : bond 0.05127 ( 272) hydrogen bonds : angle 4.89363 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.241 Fit side-chains REVERT: H 262 GLU cc_start: 0.7074 (tt0) cc_final: 0.6816 (mp0) REVERT: I 29 LYS cc_start: 0.7081 (mtpt) cc_final: 0.6457 (pttp) REVERT: I 61 GLU cc_start: 0.7832 (tt0) cc_final: 0.7372 (mt-10) REVERT: I 197 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7149 (mtt90) REVERT: J 120 MET cc_start: 0.8397 (mtm) cc_final: 0.8071 (mtm) REVERT: J 147 GLU cc_start: 0.7202 (pm20) cc_final: 0.6888 (pt0) outliers start: 5 outliers final: 0 residues processed: 111 average time/residue: 0.7353 time to fit residues: 84.0785 Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 53 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.205234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.176170 restraints weight = 2979.478| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 0.67 r_work: 0.3898 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.3598 rms_B_bonded: 4.82 restraints_weight: 0.1250 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5197 Z= 0.115 Angle : 0.526 5.293 7033 Z= 0.276 Chirality : 0.039 0.141 775 Planarity : 0.004 0.036 901 Dihedral : 4.653 53.105 689 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.18 % Allowed : 10.65 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.34), residues: 618 helix: 2.01 (0.28), residues: 345 sheet: 0.95 (1.07), residues: 15 loop : 0.49 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 63 TYR 0.018 0.002 TYR I 91 PHE 0.014 0.002 PHE I 30 TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5197) covalent geometry : angle 0.52584 ( 7033) hydrogen bonds : bond 0.04472 ( 272) hydrogen bonds : angle 4.70207 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.207 Fit side-chains REVERT: H 262 GLU cc_start: 0.7045 (tt0) cc_final: 0.6693 (mp0) REVERT: H 264 GLU cc_start: 0.6754 (mp0) cc_final: 0.6488 (tp30) REVERT: I 29 LYS cc_start: 0.7121 (mtpt) cc_final: 0.6482 (pttp) REVERT: I 61 GLU cc_start: 0.7808 (tt0) cc_final: 0.7369 (mt-10) REVERT: I 189 LYS cc_start: 0.7597 (tptt) cc_final: 0.7241 (tptp) REVERT: I 197 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7088 (mtt90) REVERT: J 120 MET cc_start: 0.8382 (mtm) cc_final: 0.8111 (mtm) REVERT: J 147 GLU cc_start: 0.7143 (pm20) cc_final: 0.6852 (pt0) REVERT: J 188 ARG cc_start: 0.6361 (mpp-170) cc_final: 0.6004 (mmt90) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.7112 time to fit residues: 80.5490 Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN ** J 129 HIS ** 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 = 0.4319 r_free = 0.4319 target = 0.203045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173692 restraints weight = 2961.560| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.67 r_work: 0.3871 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3571 rms_B_bonded: 4.73 restraints_weight: 0.1250 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5197 Z= 0.140 Angle : 0.570 5.483 7033 Z= 0.298 Chirality : 0.040 0.141 775 Planarity : 0.004 0.035 901 Dihedral : 4.730 53.988 689 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.54 % Allowed : 11.37 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.33), residues: 618 helix: 2.07 (0.28), residues: 339 sheet: 0.81 (1.08), residues: 15 loop : 0.54 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 63 TYR 0.019 0.002 TYR I 91 PHE 0.018 0.002 PHE I 30 TRP 0.010 0.001 TRP J 132 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5197) covalent geometry : angle 0.57036 ( 7033) hydrogen bonds : bond 0.04886 ( 272) hydrogen bonds : angle 4.82066 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.204 Fit side-chains REVERT: I 29 LYS cc_start: 0.7185 (mtpt) cc_final: 0.6541 (pttp) REVERT: I 61 GLU cc_start: 0.7827 (tt0) cc_final: 0.7378 (mt-10) REVERT: I 189 LYS cc_start: 0.7571 (tptt) cc_final: 0.7277 (tptp) REVERT: I 197 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7097 (mtt90) REVERT: I 218 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8125 (mp) REVERT: J 62 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7588 (tp30) REVERT: J 120 MET cc_start: 0.8396 (mtm) cc_final: 0.8076 (mtm) REVERT: J 147 GLU cc_start: 0.7192 (pm20) cc_final: 0.6882 (pt0) REVERT: J 188 ARG cc_start: 0.6423 (mpp-170) cc_final: 0.6057 (mmt90) outliers start: 3 outliers final: 0 residues processed: 112 average time/residue: 0.7059 time to fit residues: 81.4288 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 62 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN ** J 129 HIS ** 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 = 0.4312 r_free = 0.4312 target = 0.202164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.173141 restraints weight = 2943.216| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 0.66 r_work: 0.3865 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3563 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5197 Z= 0.149 Angle : 0.586 5.778 7033 Z= 0.307 Chirality : 0.040 0.140 775 Planarity : 0.005 0.037 901 Dihedral : 4.772 54.169 689 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 12.09 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.34), residues: 618 helix: 1.91 (0.28), residues: 345 sheet: 0.60 (1.09), residues: 15 loop : 0.52 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 63 TYR 0.019 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.011 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5197) covalent geometry : angle 0.58560 ( 7033) hydrogen bonds : bond 0.05010 ( 272) hydrogen bonds : angle 4.87911 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.170 Fit side-chains REVERT: H 262 GLU cc_start: 0.7014 (tt0) cc_final: 0.6756 (mp0) REVERT: I 29 LYS cc_start: 0.7226 (mtpt) cc_final: 0.6560 (pttp) REVERT: I 61 GLU cc_start: 0.7813 (tt0) cc_final: 0.7366 (mt-10) REVERT: I 189 LYS cc_start: 0.7609 (tptt) cc_final: 0.7280 (tptp) REVERT: I 197 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7116 (mtt90) REVERT: I 218 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8120 (mp) REVERT: J 120 MET cc_start: 0.8411 (mtm) cc_final: 0.8080 (mtm) REVERT: J 147 GLU cc_start: 0.7185 (pm20) cc_final: 0.6865 (pt0) REVERT: J 188 ARG cc_start: 0.6470 (mpp-170) cc_final: 0.6096 (mmt90) outliers start: 6 outliers final: 1 residues processed: 114 average time/residue: 0.6919 time to fit residues: 81.1949 Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 18 GLN I 247 GLN J 129 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.199441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170982 restraints weight = 2923.741| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.65 r_work: 0.3831 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3534 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 5197 Z= 0.348 Angle : 0.834 6.588 7033 Z= 0.445 Chirality : 0.049 0.175 775 Planarity : 0.006 0.040 901 Dihedral : 5.242 53.727 689 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 11.01 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.32), residues: 618 helix: 1.13 (0.27), residues: 345 sheet: -0.19 (1.10), residues: 19 loop : 0.54 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 57 TYR 0.023 0.004 TYR I 2 PHE 0.024 0.004 PHE J 295 TRP 0.015 0.004 TRP J 132 HIS 0.011 0.003 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00767 ( 5197) covalent geometry : angle 0.83353 ( 7033) hydrogen bonds : bond 0.06834 ( 272) hydrogen bonds : angle 5.56483 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.213 Fit side-chains REVERT: H 264 GLU cc_start: 0.6878 (mp0) cc_final: 0.6636 (mp0) REVERT: I 29 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6580 (pptt) REVERT: I 61 GLU cc_start: 0.7813 (tt0) cc_final: 0.7343 (mt-10) REVERT: I 218 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8139 (mp) REVERT: J 62 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: J 120 MET cc_start: 0.8468 (mtm) cc_final: 0.8186 (mtm) REVERT: J 147 GLU cc_start: 0.7323 (pm20) cc_final: 0.6951 (pt0) REVERT: J 188 ARG cc_start: 0.6642 (mpp-170) cc_final: 0.6235 (mmt90) outliers start: 9 outliers final: 2 residues processed: 115 average time/residue: 0.7168 time to fit residues: 84.9081 Evaluate side-chains 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 62 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.203942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.175898 restraints weight = 2910.612| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 0.64 r_work: 0.3889 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.3591 rms_B_bonded: 4.52 restraints_weight: 0.1250 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5197 Z= 0.148 Angle : 0.601 6.619 7033 Z= 0.314 Chirality : 0.041 0.144 775 Planarity : 0.005 0.038 901 Dihedral : 4.905 52.990 689 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.54 % Allowed : 12.45 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.33), residues: 618 helix: 1.79 (0.28), residues: 339 sheet: 0.52 (1.02), residues: 15 loop : 0.56 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 63 TYR 0.020 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.013 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5197) covalent geometry : angle 0.60107 ( 7033) hydrogen bonds : bond 0.05023 ( 272) hydrogen bonds : angle 5.03877 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.198 Fit side-chains REVERT: H 262 GLU cc_start: 0.6883 (tt0) cc_final: 0.6595 (mp0) REVERT: I 29 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6603 (pttp) REVERT: I 189 LYS cc_start: 0.7584 (tptt) cc_final: 0.7314 (tptp) REVERT: I 197 ARG cc_start: 0.7461 (mtp180) cc_final: 0.7026 (mtt90) REVERT: J 120 MET cc_start: 0.8396 (mtm) cc_final: 0.8145 (mtm) REVERT: J 147 GLU cc_start: 0.7236 (pm20) cc_final: 0.6891 (pt0) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.7152 time to fit residues: 82.4888 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.204044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.175659 restraints weight = 2933.374| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 0.65 r_work: 0.3884 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.3592 rms_B_bonded: 4.43 restraints_weight: 0.1250 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5197 Z= 0.154 Angle : 0.619 8.214 7033 Z= 0.321 Chirality : 0.041 0.142 775 Planarity : 0.005 0.037 901 Dihedral : 4.891 53.998 689 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.54 % Allowed : 12.09 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.34), residues: 618 helix: 1.77 (0.28), residues: 345 sheet: 0.42 (1.00), residues: 15 loop : 0.57 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 57 TYR 0.020 0.002 TYR I 91 PHE 0.017 0.002 PHE I 30 TRP 0.012 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5197) covalent geometry : angle 0.61870 ( 7033) hydrogen bonds : bond 0.05081 ( 272) hydrogen bonds : angle 5.02610 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.189 Fit side-chains REVERT: H 262 GLU cc_start: 0.6845 (tt0) cc_final: 0.6580 (mp0) REVERT: I 29 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6615 (pttp) REVERT: I 189 LYS cc_start: 0.7566 (tptt) cc_final: 0.7308 (tptp) REVERT: I 197 ARG cc_start: 0.7473 (mtp180) cc_final: 0.7050 (mtt90) REVERT: J 62 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: J 120 MET cc_start: 0.8395 (mtm) cc_final: 0.8038 (mtm) REVERT: J 147 GLU cc_start: 0.7234 (pm20) cc_final: 0.6893 (pt0) REVERT: J 188 ARG cc_start: 0.6669 (mpt90) cc_final: 0.6380 (mpt90) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.7125 time to fit residues: 82.2326 Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.202013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173489 restraints weight = 2933.451| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 0.65 r_work: 0.3860 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.3562 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5197 Z= 0.212 Angle : 0.691 6.808 7033 Z= 0.364 Chirality : 0.043 0.152 775 Planarity : 0.005 0.041 901 Dihedral : 5.035 54.413 689 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.36 % Allowed : 13.00 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.33), residues: 618 helix: 1.51 (0.27), residues: 346 sheet: 0.19 (1.00), residues: 15 loop : 0.50 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 63 TYR 0.021 0.003 TYR I 91 PHE 0.020 0.002 PHE I 30 TRP 0.013 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5197) covalent geometry : angle 0.69078 ( 7033) hydrogen bonds : bond 0.05753 ( 272) hydrogen bonds : angle 5.23008 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.207 Fit side-chains REVERT: H 262 GLU cc_start: 0.6968 (tt0) cc_final: 0.6617 (mp0) REVERT: H 264 GLU cc_start: 0.6715 (mp0) cc_final: 0.6473 (mp0) REVERT: I 29 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6590 (pttp) REVERT: I 197 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7092 (mtt90) REVERT: J 62 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: J 120 MET cc_start: 0.8428 (mtm) cc_final: 0.8152 (mtm) REVERT: J 147 GLU cc_start: 0.7291 (pm20) cc_final: 0.6933 (pt0) REVERT: J 188 ARG cc_start: 0.6691 (mpt90) cc_final: 0.6447 (mpt90) outliers start: 2 outliers final: 1 residues processed: 112 average time/residue: 0.7212 time to fit residues: 83.5346 Evaluate side-chains 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 281 GLN I 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.201872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.173305 restraints weight = 2925.359| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 0.65 r_work: 0.3859 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.3560 rms_B_bonded: 4.50 restraints_weight: 0.1250 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5197 Z= 0.222 Angle : 0.703 6.802 7033 Z= 0.370 Chirality : 0.044 0.153 775 Planarity : 0.005 0.039 901 Dihedral : 5.070 54.088 689 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.36 % Allowed : 12.64 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.33), residues: 618 helix: 1.42 (0.27), residues: 346 sheet: 0.14 (1.02), residues: 15 loop : 0.49 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 63 TYR 0.021 0.003 TYR I 91 PHE 0.020 0.003 PHE I 30 TRP 0.013 0.003 TRP J 132 HIS 0.010 0.002 HIS J 131 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 5197) covalent geometry : angle 0.70320 ( 7033) hydrogen bonds : bond 0.05831 ( 272) hydrogen bonds : angle 5.27361 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.88 seconds wall clock time: 66 minutes 9.15 seconds (3969.15 seconds total)