Starting phenix.real_space_refine on Mon Sep 23 20:40:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/09_2024/8p79_17522.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/09_2024/8p79_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/09_2024/8p79_17522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/09_2024/8p79_17522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/09_2024/8p79_17522.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p79_17522/09_2024/8p79_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-5461/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: 4.22, per 1000 atoms: 0.80 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: 1.30 Conformation dependent library (CDL) restraints added in 620.1 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: 0.54 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: 1.36 Time building geometry restraints manager: 1.51 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.660 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:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.630 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: 1.6823 time to fit residues: 230.9107 Evaluate side-chains 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.654 Fit side-chains REVERT: I 18 GLN cc_start: 0.7176 (tt0) cc_final: 0.6970 (tt0) REVERT: I 29 LYS cc_start: 0.6716 (mtpt) cc_final: 0.5802 (pttp) REVERT: I 62 LYS cc_start: 0.7577 (mtpp) cc_final: 0.7285 (mmtt) REVERT: I 77 ARG cc_start: 0.6710 (mmp80) cc_final: 0.6209 (ptt180) REVERT: I 189 LYS cc_start: 0.7425 (tttm) cc_final: 0.7074 (tptp) REVERT: I 197 ARG cc_start: 0.7246 (mtp85) cc_final: 0.6646 (mtt90) REVERT: I 223 ARG cc_start: 0.6612 (ttt-90) cc_final: 0.6178 (mpt180) REVERT: I 234 GLU cc_start: 0.6234 (pt0) cc_final: 0.6005 (mm-30) REVERT: J 25 THR cc_start: 0.7210 (OUTLIER) cc_final: 0.7004 (m) REVERT: J 120 MET cc_start: 0.8124 (mtm) cc_final: 0.7845 (mtm) REVERT: J 147 GLU cc_start: 0.7121 (pm20) cc_final: 0.6676 (pt0) REVERT: J 219 LEU cc_start: 0.6019 (mm) cc_final: 0.5771 (tp) outliers start: 5 outliers final: 1 residues processed: 118 average time/residue: 1.6060 time to fit residues: 195.6366 Evaluate side-chains 113 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 THR 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 31 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5197 Z= 0.208 Angle : 0.583 5.554 7033 Z= 0.308 Chirality : 0.041 0.143 775 Planarity : 0.005 0.040 901 Dihedral : 4.904 53.647 690 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 9.75 % 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: 1.68 (0.33), residues: 618 helix: 1.79 (0.28), residues: 345 sheet: -0.12 (1.08), residues: 20 loop : 0.40 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.019 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 114 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.611 Fit side-chains REVERT: H 281 GLN cc_start: 0.7215 (tt0) cc_final: 0.6975 (tt0) REVERT: I 18 GLN cc_start: 0.7149 (tt0) cc_final: 0.6942 (tt0) REVERT: I 29 LYS cc_start: 0.6816 (mtpt) cc_final: 0.5881 (pttp) REVERT: I 62 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7266 (mmtt) REVERT: I 77 ARG cc_start: 0.6754 (mmp80) cc_final: 0.6229 (ptt180) REVERT: I 186 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7348 (tp) REVERT: I 189 LYS cc_start: 0.7374 (tttm) cc_final: 0.7115 (tptt) REVERT: I 197 ARG cc_start: 0.7241 (mtp85) cc_final: 0.6641 (mtt90) REVERT: I 223 ARG cc_start: 0.6639 (ttt-90) cc_final: 0.6146 (mmt90) REVERT: J 25 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.7055 (m) REVERT: J 62 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: J 120 MET cc_start: 0.8141 (mtm) cc_final: 0.7793 (mtm) REVERT: J 147 GLU cc_start: 0.7145 (pm20) cc_final: 0.6716 (pt0) REVERT: J 188 ARG cc_start: 0.6089 (mpp-170) cc_final: 0.5451 (mmt90) REVERT: J 219 LEU cc_start: 0.6017 (mm) cc_final: 0.5778 (tp) outliers start: 6 outliers final: 0 residues processed: 113 average time/residue: 1.6356 time to fit residues: 190.7747 Evaluate side-chains 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain J residue 25 THR 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 55 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2211 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= 0.180 Angle : 0.542 5.255 7033 Z= 0.286 Chirality : 0.040 0.142 775 Planarity : 0.004 0.037 901 Dihedral : 4.734 53.602 689 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.03 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: 1.92 (0.34), residues: 618 helix: 1.95 (0.28), residues: 345 sheet: -0.07 (1.06), residues: 20 loop : 0.58 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.007 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 112 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.670 Fit side-chains REVERT: H 262 GLU cc_start: 0.6539 (tt0) cc_final: 0.6218 (mp0) REVERT: H 281 GLN cc_start: 0.7158 (tt0) cc_final: 0.6931 (tt0) REVERT: I 18 GLN cc_start: 0.7147 (tt0) cc_final: 0.6939 (tt0) REVERT: I 29 LYS cc_start: 0.6893 (mtpt) cc_final: 0.5951 (pttp) REVERT: I 62 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7266 (mmtt) REVERT: I 77 ARG cc_start: 0.6829 (mmp80) cc_final: 0.6322 (ptt180) REVERT: I 189 LYS cc_start: 0.7420 (tttm) cc_final: 0.7126 (tptt) REVERT: I 197 ARG cc_start: 0.7209 (mtp85) cc_final: 0.6572 (mtt90) REVERT: I 223 ARG cc_start: 0.6643 (ttt-90) cc_final: 0.6144 (mmt90) REVERT: J 41 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7433 (ttmm) REVERT: J 120 MET cc_start: 0.8128 (mtm) cc_final: 0.7795 (mtm) REVERT: J 147 GLU cc_start: 0.7130 (pm20) cc_final: 0.6718 (pt0) REVERT: J 188 ARG cc_start: 0.6080 (mpp-170) cc_final: 0.5455 (mmt90) REVERT: J 219 LEU cc_start: 0.5982 (mm) cc_final: 0.5746 (tp) REVERT: J 298 ARG cc_start: 0.6993 (mpp-170) cc_final: 0.6598 (mpp-170) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 1.8732 time to fit residues: 216.6455 Evaluate side-chains 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2241 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= 0.313 Angle : 0.683 5.936 7033 Z= 0.360 Chirality : 0.044 0.151 775 Planarity : 0.005 0.038 901 Dihedral : 5.033 54.532 689 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 9.93 % Favored : 88.27 % 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: 1.61 (0.33), residues: 618 helix: 1.63 (0.27), residues: 339 sheet: -0.14 (1.11), residues: 20 loop : 0.57 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.021 0.003 PHE I 30 TYR 0.020 0.003 TYR I 2 ARG 0.007 0.001 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 117 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.633 Fit side-chains REVERT: H 281 GLN cc_start: 0.7108 (tt0) cc_final: 0.6906 (tt0) REVERT: I 29 LYS cc_start: 0.6940 (mtpt) cc_final: 0.6005 (pttp) REVERT: I 62 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7309 (mmtt) REVERT: I 77 ARG cc_start: 0.6868 (mmp80) cc_final: 0.6333 (ptt180) REVERT: I 186 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7325 (tp) REVERT: I 189 LYS cc_start: 0.7370 (tttm) cc_final: 0.7070 (tptt) REVERT: I 223 ARG cc_start: 0.6635 (ttt-90) cc_final: 0.6116 (mmt90) REVERT: J 41 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7479 (ttmm) REVERT: J 62 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: J 120 MET cc_start: 0.8192 (mtm) cc_final: 0.7885 (mtm) REVERT: J 147 GLU cc_start: 0.7178 (pm20) cc_final: 0.6724 (pt0) REVERT: J 188 ARG cc_start: 0.6112 (mpp-170) cc_final: 0.5471 (mmt90) REVERT: J 298 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6785 (mtp85) outliers start: 10 outliers final: 2 residues processed: 114 average time/residue: 1.5691 time to fit residues: 184.6613 Evaluate side-chains 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 307 GLN Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 298 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN I 247 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2363 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= 0.198 Angle : 0.573 5.862 7033 Z= 0.300 Chirality : 0.041 0.143 775 Planarity : 0.004 0.037 901 Dihedral : 4.821 53.619 689 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 10.47 % Favored : 88.27 % 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: 1.84 (0.34), residues: 618 helix: 1.82 (0.28), residues: 345 sheet: 0.92 (1.15), residues: 15 loop : 0.55 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 132 HIS 0.006 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.008 0.000 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 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.602 Fit side-chains REVERT: H 262 GLU cc_start: 0.6404 (tt0) cc_final: 0.6059 (mp0) REVERT: I 29 LYS cc_start: 0.6932 (mtpt) cc_final: 0.5979 (pttp) REVERT: I 62 LYS cc_start: 0.7589 (mtpp) cc_final: 0.7273 (mmtt) REVERT: I 77 ARG cc_start: 0.6825 (mmp80) cc_final: 0.6315 (ptt180) REVERT: I 189 LYS cc_start: 0.7401 (tttm) cc_final: 0.7104 (tptt) REVERT: I 197 ARG cc_start: 0.7264 (mtp180) cc_final: 0.6598 (mtt90) REVERT: I 223 ARG cc_start: 0.6619 (ttt-90) cc_final: 0.6145 (mmt90) REVERT: J 41 LYS cc_start: 0.7688 (ttpt) cc_final: 0.7473 (ttmm) REVERT: J 120 MET cc_start: 0.8141 (mtm) cc_final: 0.7777 (mtm) REVERT: J 147 GLU cc_start: 0.7131 (pm20) cc_final: 0.6700 (pt0) REVERT: J 188 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5498 (mmt90) REVERT: J 219 LEU cc_start: 0.5982 (mm) cc_final: 0.5748 (tp) outliers start: 7 outliers final: 1 residues processed: 109 average time/residue: 1.5760 time to fit residues: 177.4210 Evaluate side-chains 103 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 188 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 247 GLN ** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5197 Z= 0.304 Angle : 0.671 5.944 7033 Z= 0.354 Chirality : 0.043 0.152 775 Planarity : 0.005 0.039 901 Dihedral : 5.031 54.435 689 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.26 % Allowed : 11.01 % Favored : 87.73 % 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: 1.52 (0.33), residues: 618 helix: 1.50 (0.27), residues: 346 sheet: -0.20 (1.08), residues: 20 loop : 0.59 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 132 HIS 0.010 0.002 HIS J 131 PHE 0.020 0.003 PHE I 30 TYR 0.021 0.003 TYR I 2 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 110 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.637 Fit side-chains REVERT: H 265 MET cc_start: 0.7616 (mmt) cc_final: 0.7365 (mmm) REVERT: I 29 LYS cc_start: 0.6973 (mtpt) cc_final: 0.6033 (pttp) REVERT: I 62 LYS cc_start: 0.7609 (mtpp) cc_final: 0.7312 (mmtt) REVERT: I 77 ARG cc_start: 0.6870 (mmp80) cc_final: 0.6343 (ptt180) REVERT: I 189 LYS cc_start: 0.7374 (tttm) cc_final: 0.7074 (tptt) REVERT: I 223 ARG cc_start: 0.6682 (ttt-90) cc_final: 0.6149 (mmt90) REVERT: I 269 GLU cc_start: 0.6212 (tp30) cc_final: 0.5915 (tt0) REVERT: J 41 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7472 (ttmm) REVERT: J 62 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: J 120 MET cc_start: 0.8191 (mtm) cc_final: 0.7893 (mtm) REVERT: J 147 GLU cc_start: 0.7210 (pm20) cc_final: 0.6742 (pt0) REVERT: J 188 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5883 (mpt90) outliers start: 7 outliers final: 1 residues processed: 107 average time/residue: 1.5869 time to fit residues: 175.5314 Evaluate side-chains 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 188 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2451 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= 0.219 Angle : 0.602 6.328 7033 Z= 0.314 Chirality : 0.041 0.145 775 Planarity : 0.005 0.038 901 Dihedral : 4.905 54.325 689 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.72 % Allowed : 11.37 % 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: 1.79 (0.33), residues: 618 helix: 1.76 (0.28), residues: 345 sheet: 0.89 (1.14), residues: 15 loop : 0.55 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 132 HIS 0.006 0.002 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.020 0.002 TYR I 91 ARG 0.008 0.000 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 112 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: H 262 GLU cc_start: 0.6400 (tt0) cc_final: 0.6064 (mp0) REVERT: H 265 MET cc_start: 0.7564 (mmt) cc_final: 0.7317 (mmm) REVERT: I 29 LYS cc_start: 0.6984 (mtpt) cc_final: 0.6016 (pttp) REVERT: I 62 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7282 (mmtt) REVERT: I 189 LYS cc_start: 0.7368 (tttm) cc_final: 0.7056 (tptt) REVERT: I 197 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6607 (mtt90) REVERT: I 223 ARG cc_start: 0.6644 (ttt-90) cc_final: 0.6153 (mmt90) REVERT: I 269 GLU cc_start: 0.6118 (tp30) cc_final: 0.5850 (tt0) REVERT: J 41 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7467 (ttmm) REVERT: J 120 MET cc_start: 0.8156 (mtm) cc_final: 0.7770 (mtm) REVERT: J 147 GLU cc_start: 0.7195 (pm20) cc_final: 0.6744 (pt0) REVERT: J 188 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5943 (mpt180) REVERT: J 219 LEU cc_start: 0.5983 (mm) cc_final: 0.5753 (tp) outliers start: 4 outliers final: 1 residues processed: 111 average time/residue: 1.6298 time to fit residues: 186.9165 Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 188 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.0570 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5197 Z= 0.268 Angle : 0.641 6.662 7033 Z= 0.337 Chirality : 0.042 0.147 775 Planarity : 0.005 0.040 901 Dihedral : 4.985 54.497 689 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.18 % Allowed : 12.27 % 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: 1.65 (0.33), residues: 618 helix: 1.62 (0.28), residues: 346 sheet: -0.21 (1.07), residues: 20 loop : 0.63 (0.39), residues: 252 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 0.019 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.010 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 107 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: H 262 GLU cc_start: 0.6399 (tt0) cc_final: 0.6011 (mp0) REVERT: H 265 MET cc_start: 0.7604 (mmt) cc_final: 0.7367 (mmm) REVERT: I 29 LYS cc_start: 0.6997 (mtpt) cc_final: 0.6047 (pttp) REVERT: I 62 LYS cc_start: 0.7594 (mtpp) cc_final: 0.7297 (mmtt) REVERT: I 189 LYS cc_start: 0.7387 (tttm) cc_final: 0.7088 (tptt) REVERT: I 223 ARG cc_start: 0.6660 (ttt-90) cc_final: 0.6148 (mmt90) REVERT: I 269 GLU cc_start: 0.6107 (tp30) cc_final: 0.5857 (tt0) REVERT: J 41 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7496 (ttmm) REVERT: J 120 MET cc_start: 0.8181 (mtm) cc_final: 0.7882 (mtm) REVERT: J 147 GLU cc_start: 0.7227 (pm20) cc_final: 0.6762 (pt0) REVERT: J 188 ARG cc_start: 0.6177 (mpp-170) cc_final: 0.5882 (mpt90) REVERT: J 219 LEU cc_start: 0.5971 (mm) cc_final: 0.5743 (tp) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 1.5542 time to fit residues: 171.9016 Evaluate side-chains 108 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2387 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= 0.263 Angle : 0.638 6.956 7033 Z= 0.336 Chirality : 0.042 0.146 775 Planarity : 0.005 0.039 901 Dihedral : 4.967 54.436 689 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 0.54 % Allowed : 12.09 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.33), residues: 618 helix: 1.63 (0.28), residues: 346 sheet: 0.66 (1.13), residues: 15 loop : 0.53 (0.39), residues: 257 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 0.018 0.002 PHE I 30 TYR 0.021 0.002 TYR I 91 ARG 0.010 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 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.623 Fit side-chains REVERT: H 262 GLU cc_start: 0.6397 (tt0) cc_final: 0.6005 (mp0) REVERT: H 265 MET cc_start: 0.7605 (mmt) cc_final: 0.7360 (mmm) REVERT: I 29 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6024 (pttp) REVERT: I 62 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7293 (mmtt) REVERT: I 77 ARG cc_start: 0.6872 (mmp80) cc_final: 0.6347 (ptt180) REVERT: I 189 LYS cc_start: 0.7385 (tttm) cc_final: 0.7086 (tptt) REVERT: I 223 ARG cc_start: 0.6655 (ttt-90) cc_final: 0.6142 (mmt90) REVERT: I 269 GLU cc_start: 0.6100 (tp30) cc_final: 0.5855 (tt0) REVERT: J 41 LYS cc_start: 0.7716 (ttpt) cc_final: 0.7481 (ttmm) REVERT: J 120 MET cc_start: 0.8178 (mtm) cc_final: 0.7885 (mtm) REVERT: J 147 GLU cc_start: 0.7217 (pm20) cc_final: 0.6769 (pt0) REVERT: J 188 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5506 (mmt90) REVERT: J 219 LEU cc_start: 0.5968 (mm) cc_final: 0.5746 (tp) outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 1.5294 time to fit residues: 170.7429 Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 188 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 33 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 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 = 0.4340 r_free = 0.4340 target = 0.204906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176744 restraints weight = 2912.248| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 0.65 r_work: 0.3896 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.3600 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2466 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= 0.199 Angle : 0.583 7.155 7033 Z= 0.304 Chirality : 0.040 0.146 775 Planarity : 0.005 0.038 901 Dihedral : 4.838 54.389 689 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.62 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: 1.92 (0.34), residues: 618 helix: 1.88 (0.28), residues: 345 sheet: 0.87 (1.13), 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 0.006 0.001 HIS J 131 PHE 0.015 0.002 PHE I 30 TYR 0.019 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: 3692.86 seconds wall clock time: 65 minutes 0.15 seconds (3900.15 seconds total)