Starting phenix.real_space_refine on Tue Sep 24 13:49:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/09_2024/6wut_21918.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/09_2024/6wut_21918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/09_2024/6wut_21918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/09_2024/6wut_21918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/09_2024/6wut_21918.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wut_21918/09_2024/6wut_21918.cif" } resolution = 3.0 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= 0.004 sd= 0.147 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 16 5.16 5 C 5217 2.51 5 N 1463 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8218 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2295 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 22, 'TRANS': 273} Chain breaks: 2 Chain: "B" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3295 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "C" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2628 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 25, 'TRANS': 322} Chain breaks: 3 Time building chain proxies: 5.36, per 1000 atoms: 0.65 Number of scatterers: 8218 At special positions: 0 Unit cell: (93.28, 127.2, 113.42, 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 16 16.00 O 1522 8.00 N 1463 7.00 C 5217 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: 2.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 11 sheets defined 38.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.312A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.688A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 193 through 213 Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.642A pdb=" N GLY A 233 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 234 " --> pdb=" O ALA A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 234' Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.585A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.545A pdb=" N THR A 265 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.070A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.550A pdb=" N GLU A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.976A pdb=" N PHE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 95 Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.586A pdb=" N ASP B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.958A pdb=" N THR B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 123 Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.590A pdb=" N LEU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.649A pdb=" N GLY C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.589A pdb=" N ALA C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.797A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 4.169A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.693A pdb=" N ARG C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 300 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.666A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 removed outlier: 3.804A pdb=" N GLY C 319 " --> pdb=" O PRO C 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 316 through 319' Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.764A pdb=" N GLY C 327 " --> pdb=" O TRP C 324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 328 " --> pdb=" O ALA C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 357 through 378 Processing helix chain 'C' and resid 386 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 5.994A pdb=" N ARG A 30 " --> pdb=" O LEU B 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.754A pdb=" N PHE A 103 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.146A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 51 " --> pdb=" O GLN C 418 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 418 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 142 removed outlier: 3.746A pdb=" N VAL B 171 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR B 179 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 209 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 181 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 198 through 210 Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 240 removed outlier: 4.501A pdb=" N LEU B 290 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 318 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 240 removed outlier: 4.501A pdb=" N LEU B 290 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY B 318 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 338 " --> pdb=" O SER B 400 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA9, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB1, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AB2, first strand: chain 'C' and resid 37 through 41 419 hydrogen bonds defined for protein. 1173 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: 2.52 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2574 1.34 - 1.46: 1560 1.46 - 1.58: 4247 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 8408 Sorted by residual: bond pdb=" CB TRP B 244 " pdb=" CG TRP B 244 " ideal model delta sigma weight residual 1.498 1.562 -0.064 3.10e-02 1.04e+03 4.27e+00 bond pdb=" C LEU C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.30e+00 bond pdb=" CG LEU C 52 " pdb=" CD2 LEU C 52 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 bond pdb=" CB PRO C 125 " pdb=" CG PRO C 125 " ideal model delta sigma weight residual 1.492 1.413 0.079 5.00e-02 4.00e+02 2.47e+00 bond pdb=" CB PRO C 155 " pdb=" CG PRO C 155 " ideal model delta sigma weight residual 1.492 1.418 0.074 5.00e-02 4.00e+02 2.20e+00 ... (remaining 8403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 11059 2.08 - 4.16: 315 4.16 - 6.24: 51 6.24 - 8.32: 9 8.32 - 10.40: 4 Bond angle restraints: 11438 Sorted by residual: angle pdb=" N LEU C 284 " pdb=" CA LEU C 284 " pdb=" C LEU C 284 " ideal model delta sigma weight residual 109.81 120.21 -10.40 2.21e+00 2.05e-01 2.22e+01 angle pdb=" N PHE A 27 " pdb=" CA PHE A 27 " pdb=" C PHE A 27 " ideal model delta sigma weight residual 109.81 119.99 -10.18 2.21e+00 2.05e-01 2.12e+01 angle pdb=" N LEU C 152 " pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 113.57 119.01 -5.44 1.38e+00 5.25e-01 1.56e+01 angle pdb=" N LEU C 52 " pdb=" CA LEU C 52 " pdb=" C LEU C 52 " ideal model delta sigma weight residual 109.81 118.36 -8.55 2.21e+00 2.05e-01 1.50e+01 angle pdb=" N LEU A 101 " pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 109.81 117.75 -7.94 2.21e+00 2.05e-01 1.29e+01 ... (remaining 11433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4546 17.11 - 34.23: 333 34.23 - 51.34: 80 51.34 - 68.45: 27 68.45 - 85.57: 5 Dihedral angle restraints: 4991 sinusoidal: 1911 harmonic: 3080 Sorted by residual: dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -147.42 -32.58 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA PRO C 151 " pdb=" C PRO C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual -180.00 -148.39 -31.61 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 4988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1037 0.061 - 0.123: 212 0.123 - 0.184: 31 0.184 - 0.245: 2 0.245 - 0.306: 3 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA PHE A 27 " pdb=" N PHE A 27 " pdb=" C PHE A 27 " pdb=" CB PHE A 27 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LEU A 101 " pdb=" N LEU A 101 " pdb=" C LEU A 101 " pdb=" CB LEU A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1282 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 284 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO C 285 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 159 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.56e+00 pdb=" N PRO C 160 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 188 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO A 189 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " -0.039 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1806 2.78 - 3.31: 6664 3.31 - 3.84: 13102 3.84 - 4.37: 15538 4.37 - 4.90: 27663 Nonbonded interactions: 64773 Sorted by model distance: nonbonded pdb=" OG1 THR B 257 " pdb=" OD2 ASP B 386 " model vdw 2.253 3.040 nonbonded pdb=" O THR A 45 " pdb=" OG1 THR A 45 " model vdw 2.279 3.040 nonbonded pdb=" O HIS C 51 " pdb=" OG1 THR C 54 " model vdw 2.282 3.040 nonbonded pdb=" O PHE A 55 " pdb=" OG SER A 67 " model vdw 2.300 3.040 nonbonded pdb=" OE2 GLU C 20 " pdb=" OH TYR C 278 " model vdw 2.307 3.040 ... (remaining 64768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.008 0.079 8408 Z= 0.498 Angle : 0.887 10.405 11438 Z= 0.494 Chirality : 0.053 0.306 1285 Planarity : 0.009 0.072 1485 Dihedral : 13.929 85.566 3015 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.79 % Allowed : 9.10 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.07 (0.20), residues: 1065 helix: -2.36 (0.19), residues: 387 sheet: -2.50 (0.31), residues: 234 loop : -2.97 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 360 HIS 0.009 0.002 HIS C 73 PHE 0.036 0.003 PHE B 396 TYR 0.016 0.003 TYR A 331 ARG 0.006 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 1.391 Fit side-chains REVERT: A 206 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7735 (ttp-110) REVERT: A 312 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: B 108 PHE cc_start: 0.6868 (m-80) cc_final: 0.6612 (m-80) REVERT: B 129 SER cc_start: 0.8358 (t) cc_final: 0.7843 (p) REVERT: B 134 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8060 (mt-10) REVERT: B 155 THR cc_start: 0.8058 (m) cc_final: 0.7825 (p) REVERT: B 167 GLU cc_start: 0.7726 (pt0) cc_final: 0.7361 (pt0) REVERT: B 179 THR cc_start: 0.7843 (p) cc_final: 0.7542 (t) REVERT: B 183 TYR cc_start: 0.7702 (m-80) cc_final: 0.7360 (m-80) REVERT: B 205 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7275 (tpt170) REVERT: B 283 MET cc_start: 0.7894 (mmt) cc_final: 0.7664 (mmp) REVERT: B 378 LYS cc_start: 0.8522 (ttpp) cc_final: 0.7766 (ttpt) REVERT: B 463 ASN cc_start: 0.7928 (t0) cc_final: 0.7381 (p0) REVERT: B 486 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7500 (p0) REVERT: B 494 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8453 (mpt180) REVERT: B 498 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5902 (mt-10) REVERT: C 281 LEU cc_start: 0.8359 (mt) cc_final: 0.8154 (mm) REVERT: C 299 ARG cc_start: 0.7466 (mtp85) cc_final: 0.6799 (mmt90) REVERT: C 356 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 371 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.6527 (mtm110) REVERT: C 372 GLU cc_start: 0.7592 (pt0) cc_final: 0.7388 (pt0) outliers start: 49 outliers final: 19 residues processed: 172 average time/residue: 1.1938 time to fit residues: 218.2809 Evaluate side-chains 129 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 69 ASN A 83 ASN A 166 ASN A 178 HIS A 202 HIS A 203 GLN A 310 ASN B 209 GLN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 266 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8408 Z= 0.308 Angle : 0.656 8.503 11438 Z= 0.332 Chirality : 0.044 0.207 1285 Planarity : 0.007 0.055 1485 Dihedral : 8.397 58.768 1229 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.73 % Allowed : 13.59 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.24), residues: 1065 helix: -0.41 (0.25), residues: 402 sheet: -1.74 (0.34), residues: 227 loop : -2.36 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 360 HIS 0.004 0.001 HIS C 73 PHE 0.022 0.002 PHE A 27 TYR 0.019 0.002 TYR A 53 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 109 time to evaluate : 0.959 Fit side-chains REVERT: B 50 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6807 (pt0) REVERT: B 131 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6638 (mtt90) REVERT: B 134 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7924 (mt-10) REVERT: B 137 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7216 (mtp-110) REVERT: B 155 THR cc_start: 0.8102 (m) cc_final: 0.7822 (p) REVERT: B 167 GLU cc_start: 0.7770 (pt0) cc_final: 0.7447 (pt0) REVERT: B 179 THR cc_start: 0.7756 (p) cc_final: 0.7476 (t) REVERT: B 205 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7232 (tpt170) REVERT: B 248 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8485 (p) REVERT: B 283 MET cc_start: 0.7904 (mmt) cc_final: 0.7690 (mmp) REVERT: B 463 ASN cc_start: 0.7833 (t0) cc_final: 0.7273 (p0) REVERT: B 498 GLU cc_start: 0.6314 (mm-30) cc_final: 0.6032 (mt-10) REVERT: C 299 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6667 (mmt90) REVERT: C 371 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6471 (mtm110) REVERT: C 418 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7097 (mt0) outliers start: 40 outliers final: 18 residues processed: 137 average time/residue: 1.2087 time to fit residues: 176.2109 Evaluate side-chains 116 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 0.0980 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 209 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8408 Z= 0.170 Angle : 0.554 9.116 11438 Z= 0.278 Chirality : 0.041 0.161 1285 Planarity : 0.005 0.044 1485 Dihedral : 6.310 58.471 1202 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.84 % Allowed : 16.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.25), residues: 1065 helix: 0.67 (0.27), residues: 398 sheet: -1.30 (0.35), residues: 230 loop : -2.02 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.003 0.001 HIS C 172 PHE 0.017 0.001 PHE A 27 TYR 0.013 0.001 TYR A 53 ARG 0.004 0.000 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.912 Fit side-chains REVERT: A 206 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7664 (mtp180) REVERT: A 229 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7354 (p0) REVERT: B 50 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6824 (pt0) REVERT: B 167 GLU cc_start: 0.7742 (pt0) cc_final: 0.7394 (pt0) REVERT: B 179 THR cc_start: 0.7779 (p) cc_final: 0.7541 (t) REVERT: B 205 ARG cc_start: 0.7469 (ttm-80) cc_final: 0.7242 (tpt170) REVERT: B 283 MET cc_start: 0.7907 (mmt) cc_final: 0.7696 (mmp) REVERT: B 463 ASN cc_start: 0.7760 (t0) cc_final: 0.7133 (p0) REVERT: B 498 GLU cc_start: 0.6257 (mm-30) cc_final: 0.6016 (mt-10) REVERT: C 59 ARG cc_start: 0.7898 (mpp80) cc_final: 0.7509 (mpp80) REVERT: C 299 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6627 (mmt90) REVERT: C 371 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.6457 (mtm110) outliers start: 24 outliers final: 13 residues processed: 116 average time/residue: 1.2713 time to fit residues: 156.8204 Evaluate side-chains 103 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 97 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 402 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8408 Z= 0.162 Angle : 0.538 10.210 11438 Z= 0.268 Chirality : 0.041 0.159 1285 Planarity : 0.005 0.040 1485 Dihedral : 5.806 56.382 1193 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.55 % Allowed : 16.55 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.26), residues: 1065 helix: 1.14 (0.27), residues: 398 sheet: -1.03 (0.34), residues: 233 loop : -1.83 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 360 HIS 0.004 0.001 HIS C 172 PHE 0.016 0.001 PHE A 27 TYR 0.014 0.001 TYR A 53 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.961 Fit side-chains REVERT: A 206 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7641 (mtp180) REVERT: A 229 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7353 (p0) REVERT: A 303 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7887 (ttt-90) REVERT: B 50 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6849 (pt0) REVERT: B 131 ARG cc_start: 0.7008 (mtt-85) cc_final: 0.6703 (mtt-85) REVERT: B 169 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7741 (mp) REVERT: B 202 GLU cc_start: 0.7388 (tt0) cc_final: 0.7157 (mp0) REVERT: B 205 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7234 (tpt90) REVERT: B 283 MET cc_start: 0.7903 (mmt) cc_final: 0.7690 (mmp) REVERT: B 463 ASN cc_start: 0.7744 (t0) cc_final: 0.7094 (p0) REVERT: B 498 GLU cc_start: 0.6279 (mm-30) cc_final: 0.6028 (mt-10) REVERT: C 299 ARG cc_start: 0.7347 (mtp85) cc_final: 0.6619 (mmt90) REVERT: C 371 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6391 (mtm110) outliers start: 30 outliers final: 16 residues processed: 112 average time/residue: 1.2766 time to fit residues: 151.5846 Evaluate side-chains 102 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 GLN B 209 GLN B 358 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8408 Z= 0.235 Angle : 0.576 11.235 11438 Z= 0.288 Chirality : 0.043 0.239 1285 Planarity : 0.005 0.039 1485 Dihedral : 5.904 54.079 1193 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.26 % Allowed : 16.67 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.26), residues: 1065 helix: 1.23 (0.27), residues: 399 sheet: -0.89 (0.35), residues: 230 loop : -1.82 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 360 HIS 0.005 0.001 HIS C 172 PHE 0.015 0.001 PHE A 68 TYR 0.016 0.001 TYR A 53 ARG 0.003 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 0.919 Fit side-chains REVERT: A 229 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7381 (p0) REVERT: A 312 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: B 50 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6860 (pt0) REVERT: B 134 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 169 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7843 (mp) REVERT: B 205 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.7182 (tpt170) REVERT: B 463 ASN cc_start: 0.7757 (t0) cc_final: 0.7074 (p0) REVERT: B 498 GLU cc_start: 0.6290 (mm-30) cc_final: 0.6072 (mt-10) REVERT: C 59 ARG cc_start: 0.7948 (mpp80) cc_final: 0.7505 (mpp80) REVERT: C 296 MET cc_start: 0.7911 (mtp) cc_final: 0.7710 (mtt) REVERT: C 299 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6825 (mtt-85) REVERT: C 371 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6407 (mtm110) outliers start: 36 outliers final: 21 residues processed: 118 average time/residue: 1.3423 time to fit residues: 167.7931 Evaluate side-chains 114 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8408 Z= 0.314 Angle : 0.617 11.367 11438 Z= 0.310 Chirality : 0.045 0.223 1285 Planarity : 0.005 0.040 1485 Dihedral : 6.129 55.420 1193 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.73 % Allowed : 16.67 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.25), residues: 1065 helix: 1.06 (0.27), residues: 398 sheet: -0.91 (0.34), residues: 233 loop : -1.83 (0.26), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 360 HIS 0.006 0.001 HIS C 172 PHE 0.018 0.002 PHE A 68 TYR 0.018 0.002 TYR A 53 ARG 0.003 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 96 time to evaluate : 0.820 Fit side-chains REVERT: A 267 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7539 (mtp180) REVERT: A 312 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: B 50 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6853 (pt0) REVERT: B 134 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8074 (mt-10) REVERT: B 137 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7375 (mtp-110) REVERT: B 169 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7839 (mp) REVERT: B 205 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.7147 (tpt170) REVERT: B 283 MET cc_start: 0.7885 (mmt) cc_final: 0.7683 (mmp) REVERT: B 463 ASN cc_start: 0.7767 (t0) cc_final: 0.7033 (p0) REVERT: B 494 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.5080 (mtt180) REVERT: C 59 ARG cc_start: 0.7943 (mpp80) cc_final: 0.7502 (mpp80) REVERT: C 296 MET cc_start: 0.7991 (mtp) cc_final: 0.7752 (mtt) REVERT: C 299 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6884 (mtt-85) REVERT: C 371 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.6427 (mtt90) REVERT: C 415 GLU cc_start: 0.6746 (mp0) cc_final: 0.6327 (tt0) REVERT: C 418 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6917 (mt0) outliers start: 40 outliers final: 25 residues processed: 126 average time/residue: 1.3353 time to fit residues: 177.9625 Evaluate side-chains 120 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8408 Z= 0.202 Angle : 0.565 12.312 11438 Z= 0.281 Chirality : 0.042 0.211 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.792 53.402 1193 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.26 % Allowed : 17.49 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.26), residues: 1065 helix: 1.32 (0.27), residues: 399 sheet: -0.69 (0.35), residues: 233 loop : -1.75 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.015 0.001 PHE B 396 TYR 0.015 0.001 TYR A 53 ARG 0.003 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 0.887 Fit side-chains REVERT: A 312 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: B 50 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6865 (pt0) REVERT: B 134 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 167 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6926 (pp20) REVERT: B 178 ARG cc_start: 0.7170 (mtm110) cc_final: 0.6247 (mtm110) REVERT: B 205 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.7138 (tpt170) REVERT: B 463 ASN cc_start: 0.7711 (t0) cc_final: 0.7025 (p0) REVERT: B 498 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5865 (mt-10) REVERT: C 296 MET cc_start: 0.7955 (mtp) cc_final: 0.7732 (mtt) REVERT: C 299 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6591 (mmt90) REVERT: C 371 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6386 (mtm110) REVERT: C 418 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6936 (mt0) outliers start: 36 outliers final: 21 residues processed: 115 average time/residue: 1.3294 time to fit residues: 162.2664 Evaluate side-chains 110 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -34 MET Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.0020 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8408 Z= 0.194 Angle : 0.557 11.269 11438 Z= 0.277 Chirality : 0.042 0.202 1285 Planarity : 0.005 0.042 1485 Dihedral : 5.421 53.297 1189 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.90 % Allowed : 18.20 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.26), residues: 1065 helix: 1.42 (0.27), residues: 399 sheet: -0.58 (0.36), residues: 233 loop : -1.71 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.014 0.001 PHE B 396 TYR 0.016 0.001 TYR A 53 ARG 0.004 0.000 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 86 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.8283 (mttm) cc_final: 0.8038 (mttp) REVERT: A 312 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: B 50 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6876 (pt0) REVERT: B 134 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 178 ARG cc_start: 0.7160 (mtm110) cc_final: 0.6241 (mtm110) REVERT: B 205 ARG cc_start: 0.7454 (ttm-80) cc_final: 0.7149 (tpt170) REVERT: B 463 ASN cc_start: 0.7713 (t0) cc_final: 0.7025 (p0) REVERT: B 498 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6008 (mt-10) REVERT: C 296 MET cc_start: 0.7944 (mtp) cc_final: 0.7685 (mtt) REVERT: C 299 ARG cc_start: 0.7325 (mtp85) cc_final: 0.6582 (mmt90) REVERT: C 371 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6392 (mtm110) REVERT: C 418 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6933 (mt0) outliers start: 33 outliers final: 21 residues processed: 110 average time/residue: 1.3493 time to fit residues: 156.9008 Evaluate side-chains 106 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 63 optimal weight: 0.0370 chunk 101 optimal weight: 3.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8408 Z= 0.202 Angle : 0.567 10.708 11438 Z= 0.281 Chirality : 0.042 0.199 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.375 53.400 1189 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.66 % Allowed : 18.32 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.26), residues: 1065 helix: 1.45 (0.27), residues: 399 sheet: -0.52 (0.36), residues: 233 loop : -1.67 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.014 0.001 PHE B 396 TYR 0.017 0.001 TYR B 421 ARG 0.004 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 221 LYS cc_start: 0.8309 (mttm) cc_final: 0.8077 (mttp) REVERT: A 312 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: B 50 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6869 (pt0) REVERT: B 134 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 178 ARG cc_start: 0.7162 (mtm110) cc_final: 0.6253 (mtm110) REVERT: B 205 ARG cc_start: 0.7457 (ttm-80) cc_final: 0.7156 (tpt170) REVERT: B 246 GLN cc_start: 0.8492 (tt0) cc_final: 0.8155 (tp-100) REVERT: B 463 ASN cc_start: 0.7708 (t0) cc_final: 0.7012 (p0) REVERT: B 494 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.5003 (mtt180) REVERT: B 498 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: C -34 MET cc_start: 0.3035 (pmm) cc_final: 0.2723 (pmt) REVERT: C 296 MET cc_start: 0.7931 (mtp) cc_final: 0.7710 (mtt) REVERT: C 299 ARG cc_start: 0.7339 (mtp85) cc_final: 0.6618 (mmt90) REVERT: C 371 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6382 (mtm110) REVERT: C 418 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6934 (mt0) outliers start: 31 outliers final: 21 residues processed: 106 average time/residue: 1.4663 time to fit residues: 163.7877 Evaluate side-chains 109 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 0.0060 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8408 Z= 0.170 Angle : 0.543 10.811 11438 Z= 0.270 Chirality : 0.041 0.191 1285 Planarity : 0.005 0.041 1485 Dihedral : 5.188 52.547 1189 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.43 % Allowed : 18.56 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.26), residues: 1065 helix: 1.57 (0.27), residues: 400 sheet: -0.37 (0.36), residues: 231 loop : -1.58 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 360 HIS 0.007 0.001 HIS C 172 PHE 0.015 0.001 PHE B 396 TYR 0.014 0.001 TYR A 53 ARG 0.005 0.000 ARG B 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LYS cc_start: 0.8303 (mttm) cc_final: 0.8052 (mttp) REVERT: A 312 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: B 50 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6874 (pt0) REVERT: B 163 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: B 178 ARG cc_start: 0.7116 (mtm110) cc_final: 0.6245 (mtm110) REVERT: B 205 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.7184 (tpt170) REVERT: B 246 GLN cc_start: 0.8458 (tt0) cc_final: 0.8062 (tp-100) REVERT: B 283 MET cc_start: 0.7952 (mmt) cc_final: 0.7652 (mmp) REVERT: B 463 ASN cc_start: 0.7698 (t0) cc_final: 0.6999 (p0) REVERT: B 498 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5996 (mt-10) REVERT: C 296 MET cc_start: 0.7893 (mtp) cc_final: 0.7675 (mtt) REVERT: C 299 ARG cc_start: 0.7327 (mtp85) cc_final: 0.6590 (mmt90) REVERT: C 371 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6411 (mtm110) REVERT: C 418 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6911 (mt0) outliers start: 29 outliers final: 22 residues processed: 106 average time/residue: 1.3502 time to fit residues: 151.5134 Evaluate side-chains 109 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue -32 SER Chi-restraints excluded: chain C residue -29 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 418 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 85 optimal weight: 0.1980 chunk 35 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 184 ASN B 209 GLN B 504 GLN C 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.153033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.121216 restraints weight = 8652.791| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.72 r_work: 0.3110 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8408 Z= 0.129 Angle : 0.513 10.457 11438 Z= 0.254 Chirality : 0.040 0.183 1285 Planarity : 0.005 0.043 1485 Dihedral : 4.865 51.064 1189 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.72 % Allowed : 19.62 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.26), residues: 1065 helix: 1.87 (0.27), residues: 396 sheet: -0.18 (0.36), residues: 231 loop : -1.49 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 325 HIS 0.007 0.001 HIS C 172 PHE 0.015 0.001 PHE B 396 TYR 0.014 0.001 TYR A 53 ARG 0.005 0.000 ARG B 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.17 seconds wall clock time: 59 minutes 53.05 seconds (3593.05 seconds total)