Starting phenix.real_space_refine on Tue Feb 11 10:21:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p79_17522/02_2025/8p79_17522.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p79_17522/02_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_17522/02_2025/8p79_17522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p79_17522/02_2025/8p79_17522.map" model { file = "/net/cci-nas-00/data/ceres_data/8p79_17522/02_2025/8p79_17522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p79_17522/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.38, per 1000 atoms: 0.83 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: 1.33 Conformation dependent library (CDL) restraints added in 615.7 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: 0.49 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: 1.37 Time building geometry restraints manager: 1.48 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: 3.410 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: 0.050 Process input model: 16.690 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.770 ------------------------------------------------------------------------------- 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= 0.879 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 *********************** 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 : 0.646 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: 1.7958 time to fit residues: 246.4495 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 : 0.681 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.176444 restraints weight = 2865.097| |-----------------------------------------------------------------------------| 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= 0.193 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 *********************** 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 : 0.562 Fit side-chains REVERT: I 29 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6379 (pttp) REVERT: I 189 LYS cc_start: 0.7725 (tttm) cc_final: 0.7504 (tptp) REVERT: I 197 ARG cc_start: 0.7585 (mtp85) cc_final: 0.7161 (mtt90) REVERT: J 120 MET cc_start: 0.8370 (mtm) cc_final: 0.8118 (mtm) REVERT: J 147 GLU cc_start: 0.7233 (pm20) cc_final: 0.6877 (pt0) outliers start: 5 outliers final: 1 residues processed: 118 average time/residue: 1.5599 time to fit residues: 190.1243 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 : 0.612 ------------------------------------------------------------------------------- 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: 0.0570 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: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.202868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.173682 restraints weight = 2904.419| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 0.66 r_work: 0.3869 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3759 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: 0.7637 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5197 Z= 0.193 Angle : 0.569 5.520 7033 Z= 0.299 Chirality : 0.040 0.143 775 Planarity : 0.004 0.039 901 Dihedral : 4.850 53.357 690 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 9.93 % 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: 1.73 (0.33), residues: 618 helix: 1.83 (0.28), residues: 345 sheet: -0.11 (1.08), residues: 20 loop : 0.41 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 11 HIS 0.006 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.007 0.001 ARG I 63 *********************** 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 115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.646 Fit side-chains REVERT: I 29 LYS cc_start: 0.7093 (mtpt) cc_final: 0.6439 (pttp) REVERT: I 189 LYS cc_start: 0.7726 (tttm) cc_final: 0.7500 (tptp) REVERT: I 197 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7123 (mtt90) REVERT: J 62 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: J 120 MET cc_start: 0.8396 (mtm) cc_final: 0.8097 (mtm) REVERT: J 147 GLU cc_start: 0.7196 (pm20) cc_final: 0.6881 (pt0) REVERT: J 188 ARG cc_start: 0.6382 (mpp-170) cc_final: 0.6001 (mmt90) outliers start: 5 outliers final: 0 residues processed: 113 average time/residue: 1.6534 time to fit residues: 192.7768 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 : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0060 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.204867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.175677 restraints weight = 2976.394| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 0.67 r_work: 0.3892 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.3594 rms_B_bonded: 4.77 restraints_weight: 0.1250 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5197 Z= 0.165 Angle : 0.530 5.332 7033 Z= 0.278 Chirality : 0.040 0.140 775 Planarity : 0.004 0.036 901 Dihedral : 4.666 53.108 689 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.54 % Allowed : 10.11 % Favored : 89.35 % 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: 1.93 (0.34), residues: 618 helix: 1.97 (0.28), residues: 345 sheet: 0.95 (1.10), residues: 15 loop : 0.46 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.005 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.008 0.000 ARG I 63 *********************** 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 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.625 Fit side-chains REVERT: H 262 GLU cc_start: 0.6988 (tt0) cc_final: 0.6774 (mp0) REVERT: I 29 LYS cc_start: 0.7100 (mtpt) cc_final: 0.6484 (pttp) REVERT: I 197 ARG cc_start: 0.7516 (mtp85) cc_final: 0.7068 (mtt90) REVERT: J 120 MET cc_start: 0.8377 (mtm) cc_final: 0.8096 (mtm) REVERT: J 147 GLU cc_start: 0.7164 (pm20) cc_final: 0.6864 (pt0) REVERT: J 188 ARG cc_start: 0.6391 (mpp-170) cc_final: 0.6027 (mmt90) outliers start: 3 outliers final: 0 residues processed: 111 average time/residue: 1.6914 time to fit residues: 193.6900 Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.3350 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.206094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.177229 restraints weight = 2936.853| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 0.66 r_work: 0.3908 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.3610 rms_B_bonded: 4.80 restraints_weight: 0.1250 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5197 Z= 0.162 Angle : 0.536 5.806 7033 Z= 0.276 Chirality : 0.039 0.139 775 Planarity : 0.004 0.036 901 Dihedral : 4.589 53.531 689 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.36 % Allowed : 11.01 % Favored : 88.63 % 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: 2.14 (0.34), residues: 618 helix: 2.17 (0.28), residues: 339 sheet: 1.04 (1.05), residues: 15 loop : 0.56 (0.39), residues: 264 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 0.015 0.001 PHE I 30 TYR 0.017 0.002 TYR I 91 ARG 0.008 0.000 ARG I 63 *********************** 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 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.605 Fit side-chains REVERT: H 262 GLU cc_start: 0.6977 (tt0) cc_final: 0.6660 (mp0) REVERT: H 264 GLU cc_start: 0.6737 (mp0) cc_final: 0.6429 (tp30) REVERT: I 189 LYS cc_start: 0.7580 (tptt) cc_final: 0.7231 (tptp) REVERT: I 197 ARG cc_start: 0.7526 (mtp85) cc_final: 0.7097 (mtt90) REVERT: J 120 MET cc_start: 0.8374 (mtm) cc_final: 0.8110 (mtm) REVERT: J 188 ARG cc_start: 0.6368 (mpp-170) cc_final: 0.6018 (mmt90) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 1.7173 time to fit residues: 203.3538 Evaluate side-chains 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.2980 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.202717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173694 restraints weight = 2926.208| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 0.66 r_work: 0.3871 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3572 rms_B_bonded: 4.67 restraints_weight: 0.1250 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2543 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= 0.207 Angle : 0.577 5.492 7033 Z= 0.303 Chirality : 0.040 0.137 775 Planarity : 0.005 0.035 901 Dihedral : 4.726 54.328 689 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.90 % Allowed : 11.55 % Favored : 87.55 % 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: 1.95 (0.28), residues: 345 sheet: 0.71 (1.07), residues: 15 loop : 0.53 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 *********************** 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 113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.558 Fit side-chains REVERT: H 262 GLU cc_start: 0.7005 (tt0) cc_final: 0.6799 (mp0) REVERT: I 29 LYS cc_start: 0.7204 (ttpt) cc_final: 0.6557 (pttp) REVERT: I 189 LYS cc_start: 0.7542 (tptt) cc_final: 0.7234 (tptp) REVERT: I 197 ARG cc_start: 0.7571 (mtp85) cc_final: 0.7108 (mtt90) REVERT: J 62 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: J 120 MET cc_start: 0.8408 (mtm) cc_final: 0.8086 (mtm) REVERT: J 147 GLU cc_start: 0.7224 (pm20) cc_final: 0.6897 (pt0) REVERT: J 188 ARG cc_start: 0.6450 (mpp-170) cc_final: 0.6094 (mmt90) outliers start: 5 outliers final: 1 residues processed: 112 average time/residue: 1.7257 time to fit residues: 199.1301 Evaluate side-chains 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 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 = 0.4330 r_free = 0.4330 target = 0.204285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.176083 restraints weight = 2850.313| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 0.64 r_work: 0.3886 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work: 0.3589 rms_B_bonded: 4.46 restraints_weight: 0.1250 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2585 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= 0.220 Angle : 0.599 6.115 7033 Z= 0.314 Chirality : 0.041 0.139 775 Planarity : 0.005 0.036 901 Dihedral : 4.806 54.433 689 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % 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: 1.85 (0.33), residues: 618 helix: 1.86 (0.28), residues: 345 sheet: 0.47 (1.06), 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 0.008 0.002 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.008 0.001 ARG I 63 *********************** 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 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.653 Fit side-chains REVERT: H 262 GLU cc_start: 0.6906 (tt0) cc_final: 0.6663 (mp0) REVERT: I 29 LYS cc_start: 0.7100 (ttpt) cc_final: 0.6499 (pttp) REVERT: I 189 LYS cc_start: 0.7591 (tptt) cc_final: 0.7266 (tptp) REVERT: I 197 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7095 (mtt90) REVERT: J 62 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: J 120 MET cc_start: 0.8403 (mtm) cc_final: 0.8067 (mtm) REVERT: J 188 ARG cc_start: 0.6568 (mpp-170) cc_final: 0.6185 (mmt90) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 1.7239 time to fit residues: 183.2232 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.204263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175926 restraints weight = 2907.700| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 0.65 r_work: 0.3885 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.3585 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2589 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= 0.221 Angle : 0.607 6.974 7033 Z= 0.316 Chirality : 0.041 0.139 775 Planarity : 0.005 0.037 901 Dihedral : 4.806 53.990 689 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 0.72 % Allowed : 12.45 % 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 (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: 1.85 (0.34), residues: 618 helix: 1.84 (0.28), residues: 345 sheet: 0.42 (1.04), residues: 15 loop : 0.57 (0.39), residues: 258 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 0.020 0.002 TYR I 91 ARG 0.009 0.001 ARG I 63 *********************** 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 107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.640 Fit side-chains REVERT: H 262 GLU cc_start: 0.7006 (tt0) cc_final: 0.6749 (mp0) REVERT: I 29 LYS cc_start: 0.7128 (ttpt) cc_final: 0.6521 (pttp) REVERT: I 189 LYS cc_start: 0.7593 (tptt) cc_final: 0.7267 (tptp) REVERT: I 197 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7097 (mtt90) REVERT: I 218 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8131 (mp) REVERT: J 62 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: J 120 MET cc_start: 0.8405 (mtm) cc_final: 0.8066 (mtm) REVERT: J 188 ARG cc_start: 0.6581 (mpp-170) cc_final: 0.6199 (mmt90) outliers start: 4 outliers final: 1 residues processed: 106 average time/residue: 1.6577 time to fit residues: 181.4918 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 : 0.605 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.202665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174345 restraints weight = 2876.009| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 0.64 r_work: 0.3868 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3568 rms_B_bonded: 4.49 restraints_weight: 0.1250 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5197 Z= 0.279 Angle : 0.663 6.627 7033 Z= 0.349 Chirality : 0.043 0.144 775 Planarity : 0.005 0.038 901 Dihedral : 4.946 54.744 689 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.72 % Allowed : 12.45 % 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 (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: 1.65 (0.33), residues: 618 helix: 1.64 (0.28), residues: 346 sheet: 0.37 (1.07), residues: 15 loop : 0.54 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.007 0.001 ARG I 63 *********************** 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: 4 poor density : 108 time to evaluate : 0.630 Fit side-chains REVERT: H 262 GLU cc_start: 0.6984 (tt0) cc_final: 0.6689 (mp0) REVERT: H 264 GLU cc_start: 0.6757 (mp0) cc_final: 0.6414 (mp0) REVERT: I 29 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6514 (pttp) REVERT: I 189 LYS cc_start: 0.7651 (tptt) cc_final: 0.7336 (tptp) REVERT: I 218 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8136 (mp) REVERT: J 62 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7596 (tp30) REVERT: J 120 MET cc_start: 0.8424 (mtm) cc_final: 0.8152 (mtm) REVERT: J 188 ARG cc_start: 0.6556 (mpp-170) cc_final: 0.6194 (mmt90) outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 1.6536 time to fit residues: 189.3654 Evaluate side-chains 110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 273 ASN H 281 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 = 0.4339 r_free = 0.4339 target = 0.205131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.177048 restraints weight = 2913.160| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 0.64 r_work: 0.3900 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.3602 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5197 Z= 0.201 Angle : 0.592 7.140 7033 Z= 0.308 Chirality : 0.040 0.143 775 Planarity : 0.005 0.037 901 Dihedral : 4.790 54.303 689 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.36 % Allowed : 12.27 % 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: 1.89 (0.34), residues: 618 helix: 1.85 (0.28), residues: 345 sheet: 0.49 (1.06), residues: 15 loop : 0.63 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.008 0.001 ARG I 63 ********************** 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 108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.610 Fit side-chains REVERT: H 262 GLU cc_start: 0.6937 (tt0) cc_final: 0.6660 (mp0) REVERT: H 264 GLU cc_start: 0.6677 (mp0) cc_final: 0.6337 (mp0) REVERT: I 29 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6518 (pttp) REVERT: I 189 LYS cc_start: 0.7611 (tptt) cc_final: 0.7318 (tptp) REVERT: I 197 ARG cc_start: 0.7482 (mtp180) cc_final: 0.7045 (mtt90) REVERT: I 218 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8123 (mp) REVERT: I 229 GLU cc_start: 0.6955 (pm20) cc_final: 0.6431 (mm-30) REVERT: J 120 MET cc_start: 0.8395 (mtm) cc_final: 0.8082 (mtm) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 1.6754 time to fit residues: 184.9703 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 : 0.646 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.0030 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.203879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175611 restraints weight = 2884.171| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 0.64 r_work: 0.3882 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3584 rms_B_bonded: 4.43 restraints_weight: 0.1250 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5197 Z= 0.238 Angle : 0.634 7.020 7033 Z= 0.331 Chirality : 0.041 0.142 775 Planarity : 0.005 0.041 901 Dihedral : 4.887 54.812 689 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % 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: 1.77 (0.33), residues: 618 helix: 1.74 (0.28), residues: 345 sheet: 0.27 (1.03), residues: 15 loop : 0.61 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.008 0.002 HIS J 131 PHE 0.020 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.010 0.001 ARG I 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8392.49 seconds wall clock time: 147 minutes 54.68 seconds (8874.68 seconds total)