Starting phenix.real_space_refine on Sun Apr 27 09:34:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p79_17522/04_2025/8p79_17522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p79_17522/04_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_17522/04_2025/8p79_17522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p79_17522/04_2025/8p79_17522.map" model { file = "/net/cci-nas-00/data/ceres_data/8p79_17522/04_2025/8p79_17522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p79_17522/04_2025/8p79_17522.cif" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.24, per 1000 atoms: 0.81 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: 1.23 Conformation dependent library (CDL) restraints added in 588.1 milliseconds 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: 0.65 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: 1.44 Time building geometry restraints manager: 1.45 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.840 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (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 TRP 0.032 0.007 TRP I 11 HIS 0.016 0.004 HIS I 3 PHE 0.030 0.006 PHE J 295 TYR 0.057 0.007 TYR I 2 ARG 0.017 0.001 ARG I 89 Details of bonding type rmsd hydrogen bonds : bond 0.18133 ( 272) hydrogen bonds : angle 7.26168 ( 768) covalent geometry : bond 0.01350 ( 5197) covalent geometry : angle 1.73217 ( 7033) *********************** 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 : 0.511 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: 0.6001 (pttp) 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: 0.6225 (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: 1.6708 time to fit residues: 228.8991 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 : 0.635 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.205066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176429 restraints weight = 2865.098| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 0.65 r_work: 0.3886 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work: 0.3590 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5197 Z= 0.138 Angle : 0.579 5.607 7033 Z= 0.306 Chirality : 0.041 0.147 775 Planarity : 0.004 0.038 901 Dihedral : 4.926 52.312 690 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.33), residues: 618 helix: 1.61 (0.27), residues: 339 sheet: -0.01 (1.10), residues: 20 loop : 0.25 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.005 0.001 HIS I 161 PHE 0.018 0.002 PHE J 295 TYR 0.020 0.002 TYR I 207 ARG 0.006 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 272) hydrogen bonds : angle 4.93868 ( 768) covalent geometry : bond 0.00297 ( 5197) covalent geometry : angle 0.57941 ( 7033) *********************** 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 120 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.596 Fit side-chains REVERT: I 29 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6368 (pttp) REVERT: I 189 LYS cc_start: 0.7726 (tttm) cc_final: 0.7502 (tptp) REVERT: I 197 ARG cc_start: 0.7590 (mtp85) cc_final: 0.7162 (mtt90) REVERT: J 120 MET cc_start: 0.8369 (mtm) cc_final: 0.8118 (mtm) REVERT: J 147 GLU cc_start: 0.7229 (pm20) cc_final: 0.6874 (pt0) outliers start: 5 outliers final: 1 residues processed: 118 average time/residue: 1.5464 time to fit residues: 188.4610 Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.0770 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.200806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171620 restraints weight = 2889.910| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.66 r_work: 0.3846 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3543 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5197 Z= 0.173 Angle : 0.618 5.601 7033 Z= 0.327 Chirality : 0.042 0.143 775 Planarity : 0.005 0.039 901 Dihedral : 4.986 54.034 690 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 10.11 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.33), residues: 618 helix: 1.66 (0.27), residues: 345 sheet: -0.16 (1.11), residues: 20 loop : 0.37 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.020 0.002 PHE J 295 TYR 0.019 0.002 TYR I 91 ARG 0.006 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05470 ( 272) hydrogen bonds : angle 5.04555 ( 768) covalent geometry : bond 0.00378 ( 5197) covalent geometry : angle 0.61843 ( 7033) *********************** 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.587 Fit side-chains REVERT: I 29 LYS cc_start: 0.7144 (mtpt) cc_final: 0.6507 (pttp) REVERT: I 197 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7179 (mtt90) REVERT: I 223 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6341 (mmt90) REVERT: J 62 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: J 120 MET cc_start: 0.8418 (mtm) cc_final: 0.8094 (mtm) REVERT: J 147 GLU cc_start: 0.7207 (pm20) cc_final: 0.6879 (pt0) REVERT: J 188 ARG cc_start: 0.6459 (mpp-170) cc_final: 0.6059 (mmt90) outliers start: 6 outliers final: 0 residues processed: 108 average time/residue: 1.6622 time to fit residues: 185.1300 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain J residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.3234 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.205187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176401 restraints weight = 2993.868| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 0.67 r_work: 0.3901 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work: 0.3604 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5197 Z= 0.115 Angle : 0.532 5.471 7033 Z= 0.278 Chirality : 0.040 0.143 775 Planarity : 0.004 0.037 901 Dihedral : 4.669 52.571 689 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.54 % Allowed : 10.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.34), residues: 618 helix: 1.97 (0.28), residues: 345 sheet: 1.04 (1.13), residues: 15 loop : 0.48 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.013 0.001 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.009 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 272) hydrogen bonds : angle 4.71172 ( 768) covalent geometry : bond 0.00246 ( 5197) covalent geometry : angle 0.53164 ( 7033) *********************** 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 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.618 Fit side-chains REVERT: H 262 GLU cc_start: 0.7029 (tt0) cc_final: 0.6773 (mp0) REVERT: I 189 LYS cc_start: 0.7582 (tptt) cc_final: 0.7261 (tptp) REVERT: I 197 ARG cc_start: 0.7536 (mtp85) cc_final: 0.7092 (mtt90) REVERT: J 120 MET cc_start: 0.8379 (mtm) cc_final: 0.8110 (mtm) REVERT: J 147 GLU cc_start: 0.7172 (pm20) cc_final: 0.6863 (pt0) REVERT: J 188 ARG cc_start: 0.6451 (mpp-170) cc_final: 0.6117 (mmt90) outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 1.7007 time to fit residues: 194.5940 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 : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.0570 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.202593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173534 restraints weight = 2911.559| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 0.66 r_work: 0.3867 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3567 rms_B_bonded: 4.72 restraints_weight: 0.1250 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2581 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= 0.143 Angle : 0.575 5.742 7033 Z= 0.300 Chirality : 0.040 0.140 775 Planarity : 0.004 0.036 901 Dihedral : 4.759 54.155 689 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.90 % Allowed : 11.19 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.34), residues: 618 helix: 1.92 (0.28), residues: 345 sheet: 0.84 (1.12), residues: 15 loop : 0.52 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 11 HIS 0.007 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.007 0.000 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 272) hydrogen bonds : angle 4.84285 ( 768) covalent geometry : bond 0.00314 ( 5197) covalent geometry : angle 0.57537 ( 7033) *********************** 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 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.592 Fit side-chains REVERT: H 262 GLU cc_start: 0.7021 (tt0) cc_final: 0.6694 (mp0) REVERT: I 29 LYS cc_start: 0.7162 (ttpt) cc_final: 0.6515 (pttp) REVERT: I 189 LYS cc_start: 0.7578 (tptt) cc_final: 0.7255 (tptp) REVERT: I 197 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7111 (mtt90) REVERT: J 62 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: J 120 MET cc_start: 0.8399 (mtm) cc_final: 0.8069 (mtm) REVERT: J 147 GLU cc_start: 0.7199 (pm20) cc_final: 0.6870 (pt0) REVERT: J 188 ARG cc_start: 0.6484 (mpp-170) cc_final: 0.6124 (mmt90) outliers start: 5 outliers final: 0 residues processed: 111 average time/residue: 1.6487 time to fit residues: 188.7315 Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 10 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.0070 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.201675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172872 restraints weight = 2942.469| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 0.66 r_work: 0.3861 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.3559 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2620 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= 0.153 Angle : 0.591 5.723 7033 Z= 0.310 Chirality : 0.041 0.140 775 Planarity : 0.005 0.037 901 Dihedral : 4.820 54.270 689 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.72 % Allowed : 11.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.33), residues: 618 helix: 1.87 (0.28), residues: 345 sheet: 0.57 (1.09), residues: 15 loop : 0.53 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.008 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05078 ( 272) hydrogen bonds : angle 4.91294 ( 768) covalent geometry : bond 0.00335 ( 5197) covalent geometry : angle 0.59134 ( 7033) *********************** 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.630 Fit side-chains REVERT: H 262 GLU cc_start: 0.7033 (tt0) cc_final: 0.6728 (mp0) REVERT: I 29 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6559 (pttp) REVERT: I 189 LYS cc_start: 0.7638 (tptt) cc_final: 0.7282 (tptp) REVERT: I 197 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7125 (mtt90) REVERT: I 218 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8144 (mp) REVERT: J 62 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7566 (tp30) REVERT: J 120 MET cc_start: 0.8412 (mtm) cc_final: 0.8077 (mtm) REVERT: J 147 GLU cc_start: 0.7220 (pm20) cc_final: 0.6889 (pt0) REVERT: J 188 ARG cc_start: 0.6511 (mpp-170) cc_final: 0.6138 (mmt90) outliers start: 4 outliers final: 1 residues processed: 107 average time/residue: 1.6450 time to fit residues: 181.5297 Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.0070 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.207547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179654 restraints weight = 2909.300| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 0.64 r_work: 0.3925 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3630 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2738 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= 0.115 Angle : 0.545 6.232 7033 Z= 0.283 Chirality : 0.039 0.142 775 Planarity : 0.004 0.037 901 Dihedral : 4.650 54.019 689 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 11.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.34), residues: 618 helix: 2.00 (0.28), residues: 345 sheet: 0.53 (0.98), residues: 15 loop : 0.59 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.013 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.007 0.000 ARG J 57 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 272) hydrogen bonds : angle 4.69063 ( 768) covalent geometry : bond 0.00250 ( 5197) covalent geometry : angle 0.54513 ( 7033) *********************** 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 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.623 Fit side-chains REVERT: H 262 GLU cc_start: 0.6891 (tt0) cc_final: 0.6582 (mp0) REVERT: I 29 LYS cc_start: 0.7185 (ttpt) cc_final: 0.6536 (pttp) REVERT: I 189 LYS cc_start: 0.7583 (tptt) cc_final: 0.7271 (tptp) REVERT: I 197 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7031 (mtt90) REVERT: J 120 MET cc_start: 0.8361 (mtm) cc_final: 0.8090 (mtm) REVERT: J 147 GLU cc_start: 0.7220 (pm20) cc_final: 0.6885 (pt0) REVERT: J 188 ARG cc_start: 0.6516 (mpp-170) cc_final: 0.6139 (mmt90) outliers start: 6 outliers final: 1 residues processed: 108 average time/residue: 1.6301 time to fit residues: 181.7759 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.204535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175975 restraints weight = 2904.706| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 0.65 r_work: 0.3884 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3583 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5197 Z= 0.156 Angle : 0.599 5.920 7033 Z= 0.313 Chirality : 0.041 0.137 775 Planarity : 0.005 0.037 901 Dihedral : 4.768 54.528 689 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.36 % Allowed : 12.45 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.34), residues: 618 helix: 1.89 (0.28), residues: 345 sheet: 0.25 (1.03), residues: 15 loop : 0.58 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.007 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 272) hydrogen bonds : angle 4.90847 ( 768) covalent geometry : bond 0.00344 ( 5197) covalent geometry : angle 0.59927 ( 7033) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.584 Fit side-chains REVERT: H 262 GLU cc_start: 0.6932 (tt0) cc_final: 0.6658 (mp0) REVERT: I 29 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6522 (pttp) REVERT: I 197 ARG cc_start: 0.7555 (mtp85) cc_final: 0.7084 (mtt90) REVERT: J 120 MET cc_start: 0.8406 (mtm) cc_final: 0.8071 (mtm) REVERT: J 147 GLU cc_start: 0.7213 (pm20) cc_final: 0.6879 (pt0) REVERT: J 188 ARG cc_start: 0.6571 (mpp-170) cc_final: 0.6179 (mmt90) outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 1.6328 time to fit residues: 175.3542 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 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 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 = 0.4337 r_free = 0.4337 target = 0.204934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.176751 restraints weight = 2902.997| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 0.65 r_work: 0.3893 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.3593 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5197 Z= 0.147 Angle : 0.603 7.518 7033 Z= 0.313 Chirality : 0.040 0.138 775 Planarity : 0.005 0.041 901 Dihedral : 4.770 54.389 689 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.34), residues: 618 helix: 1.87 (0.28), residues: 345 sheet: 0.35 (1.03), residues: 15 loop : 0.61 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 132 HIS 0.007 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.010 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 272) hydrogen bonds : angle 4.88534 ( 768) covalent geometry : bond 0.00325 ( 5197) covalent geometry : angle 0.60286 ( 7033) *********************** 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 104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.659 Fit side-chains REVERT: I 29 LYS cc_start: 0.7165 (ttpt) cc_final: 0.6534 (pttp) REVERT: I 189 LYS cc_start: 0.7510 (tptt) cc_final: 0.7228 (tptp) REVERT: I 197 ARG cc_start: 0.7532 (mtp85) cc_final: 0.7067 (mtt90) REVERT: I 218 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8133 (mp) REVERT: J 120 MET cc_start: 0.8405 (mtm) cc_final: 0.8081 (mtm) REVERT: J 147 GLU cc_start: 0.7202 (pm20) cc_final: 0.6847 (pt0) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 1.5834 time to fit residues: 168.5897 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.204517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176310 restraints weight = 2899.954| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 0.64 r_work: 0.3889 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.3590 rms_B_bonded: 4.58 restraints_weight: 0.1250 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5197 Z= 0.155 Angle : 0.620 7.109 7033 Z= 0.324 Chirality : 0.041 0.138 775 Planarity : 0.005 0.039 901 Dihedral : 4.830 54.943 689 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.33), residues: 618 helix: 1.94 (0.28), residues: 339 sheet: 0.34 (1.02), residues: 15 loop : 0.64 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.007 0.002 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.010 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 272) hydrogen bonds : angle 4.93800 ( 768) covalent geometry : bond 0.00345 ( 5197) covalent geometry : angle 0.61975 ( 7033) ********************** 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 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.671 Fit side-chains REVERT: H 262 GLU cc_start: 0.6806 (tt0) cc_final: 0.6504 (mp0) REVERT: I 29 LYS cc_start: 0.7128 (ttpt) cc_final: 0.6504 (pttp) REVERT: I 189 LYS cc_start: 0.7512 (tptt) cc_final: 0.7219 (tptp) REVERT: I 197 ARG cc_start: 0.7546 (mtp85) cc_final: 0.7085 (mtt90) REVERT: I 218 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8135 (mp) REVERT: I 229 GLU cc_start: 0.6969 (pm20) cc_final: 0.6430 (mm-30) REVERT: J 120 MET cc_start: 0.8403 (mtm) cc_final: 0.8069 (mtm) REVERT: J 147 GLU cc_start: 0.7217 (pm20) cc_final: 0.6874 (pt0) REVERT: J 188 ARG cc_start: 0.6646 (mpt90) cc_final: 0.6401 (mpt90) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 1.6392 time to fit residues: 171.2981 Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4313 r_free = 0.4313 target = 0.202235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173837 restraints weight = 2883.865| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.64 r_work: 0.3863 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3566 rms_B_bonded: 4.44 restraints_weight: 0.1250 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5197 Z= 0.215 Angle : 0.693 6.906 7033 Z= 0.365 Chirality : 0.043 0.147 775 Planarity : 0.005 0.039 901 Dihedral : 5.013 55.093 689 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 12.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.33), residues: 618 helix: 1.55 (0.27), residues: 346 sheet: 0.14 (1.04), residues: 15 loop : 0.57 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 177 HIS 0.011 0.002 HIS J 131 PHE 0.021 0.002 PHE I 30 TYR 0.021 0.003 TYR I 91 ARG 0.008 0.001 ARG I 63 Details of bonding type rmsd hydrogen bonds : bond 0.05722 ( 272) hydrogen bonds : angle 5.19545 ( 768) covalent geometry : bond 0.00476 ( 5197) covalent geometry : angle 0.69265 ( 7033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9190.76 seconds wall clock time: 157 minutes 26.32 seconds (9446.32 seconds total)