Starting phenix.real_space_refine on Tue Feb 11 16:21:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yho_39290/02_2025/8yho_39290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yho_39290/02_2025/8yho_39290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yho_39290/02_2025/8yho_39290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yho_39290/02_2025/8yho_39290.map" model { file = "/net/cci-nas-00/data/ceres_data/8yho_39290/02_2025/8yho_39290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yho_39290/02_2025/8yho_39290.cif" } resolution = 2.8 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= 0.008 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 15 5.16 5 C 3953 2.51 5 N 1022 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6206 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2028 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2024 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 2, 'TRANS': 244} Chain breaks: 2 Chain: "C" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2154 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 4.71, per 1000 atoms: 0.76 Number of scatterers: 6206 At special positions: 0 Unit cell: (83.78, 87.33, 100.11, 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 15 16.00 O 1216 8.00 N 1022 7.00 C 3953 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: 1.46 Conformation dependent library (CDL) restraints added in 817.0 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 57.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 229 through 246 removed outlier: 3.543A pdb=" N ILE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.554A pdb=" N ARG A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.727A pdb=" N ASP A 292 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.560A pdb=" N GLU A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 305 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.678A pdb=" N THR A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 230 through 246 Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.790A pdb=" N LYS B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.634A pdb=" N ILE B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 354 Processing helix chain 'B' and resid 358 through 369 removed outlier: 5.245A pdb=" N THR B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 401 through 423 removed outlier: 3.685A pdb=" N ASN B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 173 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 229 through 246 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.645A pdb=" N LEU C 281 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.777A pdb=" N THR C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 317 removed outlier: 3.827A pdb=" N VAL C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.761A pdb=" N LEU C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 removed outlier: 3.781A pdb=" N SER C 361 " --> pdb=" O ASN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.736A pdb=" N GLU C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 401 through 423 removed outlier: 3.910A pdb=" N LEU C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.544A pdb=" N ILE A 185 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS A 199 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N SER A 396 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL A 201 " --> pdb=" O SER A 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 186 removed outlier: 6.258A pdb=" N ILE B 185 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 201 " --> pdb=" O SER B 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 209 through 210 removed outlier: 5.196A pdb=" N ILE B 209 " --> pdb=" O GLY B 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.480A pdb=" N ILE C 185 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS C 199 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER C 396 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 201 " --> pdb=" O SER C 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 209 through 210 removed outlier: 5.359A pdb=" N ILE C 209 " --> pdb=" O GLY C 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 265 hydrogen bonds defined for protein. 786 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: 1.60 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1169 1.32 - 1.44: 1504 1.44 - 1.56: 3586 1.56 - 1.68: 5 1.68 - 1.81: 27 Bond restraints: 6291 Sorted by residual: bond pdb=" N LYS C 294 " pdb=" CA LYS C 294 " ideal model delta sigma weight residual 1.457 1.570 -0.113 1.29e-02 6.01e+03 7.68e+01 bond pdb=" CA LYS C 294 " pdb=" C LYS C 294 " ideal model delta sigma weight residual 1.523 1.630 -0.107 1.34e-02 5.57e+03 6.40e+01 bond pdb=" C THR C 284 " pdb=" O THR C 284 " ideal model delta sigma weight residual 1.234 1.311 -0.077 1.07e-02 8.73e+03 5.16e+01 bond pdb=" N ASP C 287 " pdb=" CA ASP C 287 " ideal model delta sigma weight residual 1.458 1.372 0.086 1.30e-02 5.92e+03 4.39e+01 bond pdb=" CA GLU C 303 " pdb=" C GLU C 303 " ideal model delta sigma weight residual 1.523 1.465 0.059 1.30e-02 5.92e+03 2.04e+01 ... (remaining 6286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 8303 4.56 - 9.13: 137 9.13 - 13.69: 15 13.69 - 18.26: 1 18.26 - 22.82: 4 Bond angle restraints: 8460 Sorted by residual: angle pdb=" N ASP C 287 " pdb=" CA ASP C 287 " pdb=" C ASP C 287 " ideal model delta sigma weight residual 113.55 90.73 22.82 1.26e+00 6.30e-01 3.28e+02 angle pdb=" CA LYS C 294 " pdb=" C LYS C 294 " pdb=" O LYS C 294 " ideal model delta sigma weight residual 120.51 140.28 -19.77 1.43e+00 4.89e-01 1.91e+02 angle pdb=" C LYS C 290 " pdb=" N TYR C 291 " pdb=" CA TYR C 291 " ideal model delta sigma weight residual 122.67 104.33 18.34 1.59e+00 3.96e-01 1.33e+02 angle pdb=" N ILE C 286 " pdb=" CA ILE C 286 " pdb=" C ILE C 286 " ideal model delta sigma weight residual 112.80 101.23 11.57 1.15e+00 7.56e-01 1.01e+02 angle pdb=" N LYS C 294 " pdb=" CA LYS C 294 " pdb=" C LYS C 294 " ideal model delta sigma weight residual 110.80 132.15 -21.35 2.13e+00 2.20e-01 1.00e+02 ... (remaining 8455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 3532 17.00 - 34.01: 262 34.01 - 51.01: 37 51.01 - 68.02: 14 68.02 - 85.02: 6 Dihedral angle restraints: 3851 sinusoidal: 1609 harmonic: 2242 Sorted by residual: dihedral pdb=" CA GLY C 296 " pdb=" C GLY C 296 " pdb=" N ASN C 297 " pdb=" CA ASN C 297 " ideal model delta harmonic sigma weight residual 180.00 103.43 76.57 0 5.00e+00 4.00e-02 2.35e+02 dihedral pdb=" CA ASN C 297 " pdb=" C ASN C 297 " pdb=" N MET C 298 " pdb=" CA MET C 298 " ideal model delta harmonic sigma weight residual -180.00 -114.55 -65.45 0 5.00e+00 4.00e-02 1.71e+02 dihedral pdb=" CA SER C 293 " pdb=" C SER C 293 " pdb=" N LYS C 294 " pdb=" CA LYS C 294 " ideal model delta harmonic sigma weight residual 180.00 125.39 54.61 0 5.00e+00 4.00e-02 1.19e+02 ... (remaining 3848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 948 0.185 - 0.370: 18 0.370 - 0.554: 0 0.554 - 0.739: 2 0.739 - 0.924: 1 Chirality restraints: 969 Sorted by residual: chirality pdb=" CA LYS C 294 " pdb=" N LYS C 294 " pdb=" C LYS C 294 " pdb=" CB LYS C 294 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.13e+01 chirality pdb=" CA TYR C 291 " pdb=" N TYR C 291 " pdb=" C TYR C 291 " pdb=" CB TYR C 291 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA SER C 293 " pdb=" N SER C 293 " pdb=" C SER C 293 " pdb=" CB SER C 293 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.92e+00 ... (remaining 966 not shown) Planarity restraints: 1076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 377 " 0.026 2.00e-02 2.50e+03 2.71e-02 1.29e+01 pdb=" CG PHE B 377 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE B 377 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 377 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 377 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 377 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE B 377 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 227 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLU C 227 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU C 227 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C 228 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 281 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.17e+01 pdb=" C LEU C 281 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 281 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP C 282 " 0.020 2.00e-02 2.50e+03 ... (remaining 1073 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1134 2.74 - 3.28: 6381 3.28 - 3.82: 10706 3.82 - 4.36: 13455 4.36 - 4.90: 21649 Nonbonded interactions: 53325 Sorted by model distance: nonbonded pdb=" N ASP C 287 " pdb=" N THR C 288 " model vdw 2.200 2.560 nonbonded pdb=" O LEU A 350 " pdb=" OG SER A 353 " model vdw 2.214 3.040 nonbonded pdb=" N ILE C 286 " pdb=" N ASP C 287 " model vdw 2.223 2.560 nonbonded pdb=" O PHE B 306 " pdb=" OG SER B 309 " model vdw 2.253 3.040 nonbonded pdb=" O SER B 361 " pdb=" OG SER C 324 " model vdw 2.265 3.040 ... (remaining 53320 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 179 through 294 or resid 296 through 318 or resid 321 thro \ ugh 428)) selection = (chain 'B' and (resid 179 through 327 or resid 329 through 428)) selection = (chain 'C' and (resid 179 through 294 or resid 296 through 327 or resid 329 thro \ ugh 428)) } 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=0.00 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.720 Find NCS groups from input model: 0.290 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.018 0.142 6291 Z= 1.123 Angle : 1.523 22.821 8460 Z= 0.893 Chirality : 0.083 0.924 969 Planarity : 0.007 0.039 1076 Dihedral : 12.890 85.019 2387 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.21 % Favored : 91.25 % Rotamer: Outliers : 1.83 % Allowed : 6.35 % Favored : 91.82 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.48 % 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: -4.81 (0.23), residues: 743 helix: -3.43 (0.16), residues: 419 sheet: -2.92 (0.74), residues: 25 loop : -2.59 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP A 253 HIS 0.014 0.002 HIS B 184 PHE 0.059 0.005 PHE B 377 TYR 0.032 0.005 TYR B 240 ARG 0.015 0.003 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 TYR cc_start: 0.8383 (t80) cc_final: 0.8059 (t80) REVERT: B 287 ASP cc_start: 0.8590 (t0) cc_final: 0.8375 (OUTLIER) REVERT: B 291 TYR cc_start: 0.7465 (t80) cc_final: 0.6969 (t80) REVERT: B 308 GLU cc_start: 0.8886 (tt0) cc_final: 0.8563 (tm-30) REVERT: B 312 ASN cc_start: 0.7863 (p0) cc_final: 0.7544 (p0) REVERT: B 362 TYR cc_start: 0.8374 (m-80) cc_final: 0.8008 (m-80) REVERT: B 395 TYR cc_start: 0.8749 (m-10) cc_final: 0.8507 (m-10) REVERT: B 405 LEU cc_start: 0.9260 (tt) cc_final: 0.9045 (tm) REVERT: C 240 TYR cc_start: 0.8757 (m-80) cc_final: 0.8539 (m-80) REVERT: C 291 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6544 (t80) outliers start: 13 outliers final: 3 residues processed: 140 average time/residue: 1.2484 time to fit residues: 183.0760 Evaluate side-chains 74 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 321 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN B 180 ASN B 213 ASN B 221 ASN B 242 ASN B 246 ASN B 338 ASN C 174 ASN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 372 ASN C 379 ASN C 420 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.135640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097655 restraints weight = 12860.790| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.67 r_work: 0.3404 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6291 Z= 0.242 Angle : 0.745 9.379 8460 Z= 0.392 Chirality : 0.045 0.221 969 Planarity : 0.004 0.025 1076 Dihedral : 7.077 45.285 803 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.65 % Favored : 94.08 % Rotamer: Outliers : 3.39 % Allowed : 11.85 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -2.99 (0.27), residues: 743 helix: -1.56 (0.21), residues: 432 sheet: -3.38 (0.68), residues: 30 loop : -2.31 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 253 HIS 0.003 0.001 HIS A 184 PHE 0.027 0.002 PHE B 306 TYR 0.026 0.002 TYR A 291 ARG 0.004 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8700 (m-30) cc_final: 0.8295 (t0) REVERT: A 256 CYS cc_start: 0.9172 (m) cc_final: 0.8927 (m) REVERT: A 290 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8875 (tmmt) REVERT: A 395 TYR cc_start: 0.7661 (m-80) cc_final: 0.7257 (m-80) REVERT: B 189 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7676 (m90) REVERT: B 218 ASP cc_start: 0.8487 (m-30) cc_final: 0.8252 (m-30) REVERT: B 263 TYR cc_start: 0.8583 (t80) cc_final: 0.8311 (t80) REVERT: B 274 ARG cc_start: 0.9148 (ttp-110) cc_final: 0.8795 (ptm-80) REVERT: B 291 TYR cc_start: 0.8119 (t80) cc_final: 0.7619 (t80) REVERT: C 217 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7474 (tp40) REVERT: C 236 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: C 252 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8541 (pp20) REVERT: C 298 MET cc_start: 0.7493 (pmm) cc_final: 0.6890 (ttm) REVERT: C 406 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7455 (tm) outliers start: 24 outliers final: 3 residues processed: 128 average time/residue: 1.0133 time to fit residues: 137.4493 Evaluate side-chains 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.134705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096204 restraints weight = 12820.061| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.71 r_work: 0.3424 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6291 Z= 0.212 Angle : 0.704 11.796 8460 Z= 0.357 Chirality : 0.043 0.195 969 Planarity : 0.003 0.020 1076 Dihedral : 5.926 31.829 797 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.59 % Favored : 93.27 % Rotamer: Outliers : 3.10 % Allowed : 14.10 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.82 (0.29), residues: 743 helix: -0.62 (0.24), residues: 437 sheet: -3.05 (0.72), residues: 30 loop : -1.79 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 253 HIS 0.002 0.001 HIS B 184 PHE 0.021 0.002 PHE B 306 TYR 0.017 0.002 TYR A 362 ARG 0.009 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8715 (m-30) cc_final: 0.8282 (t0) REVERT: A 256 CYS cc_start: 0.9175 (m) cc_final: 0.8944 (m) REVERT: A 298 MET cc_start: 0.4807 (pmm) cc_final: 0.4565 (pmm) REVERT: A 363 SER cc_start: 0.8919 (m) cc_final: 0.8313 (t) REVERT: A 395 TYR cc_start: 0.7567 (m-80) cc_final: 0.7246 (m-80) REVERT: A 402 ASP cc_start: 0.8600 (m-30) cc_final: 0.8297 (p0) REVERT: B 189 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7771 (m90) REVERT: B 263 TYR cc_start: 0.8525 (t80) cc_final: 0.8299 (t80) REVERT: B 291 TYR cc_start: 0.7947 (t80) cc_final: 0.7195 (t80) REVERT: C 205 ASN cc_start: 0.9031 (m-40) cc_final: 0.8668 (m110) REVERT: C 236 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8620 (mmm) REVERT: C 305 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9083 (mmtm) REVERT: C 406 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7349 (tm) outliers start: 22 outliers final: 4 residues processed: 110 average time/residue: 0.9830 time to fit residues: 114.6575 Evaluate side-chains 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.135101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.097765 restraints weight = 12862.395| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 3.62 r_work: 0.3455 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6291 Z= 0.219 Angle : 0.696 9.604 8460 Z= 0.350 Chirality : 0.043 0.225 969 Planarity : 0.003 0.019 1076 Dihedral : 5.501 28.444 797 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.95 % Allowed : 15.23 % Favored : 80.82 % 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: -1.38 (0.30), residues: 743 helix: -0.26 (0.24), residues: 446 sheet: -2.83 (0.78), residues: 30 loop : -1.66 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 253 HIS 0.002 0.000 HIS B 184 PHE 0.032 0.002 PHE B 377 TYR 0.016 0.002 TYR A 362 ARG 0.004 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8703 (m-30) cc_final: 0.8316 (t0) REVERT: A 256 CYS cc_start: 0.9177 (m) cc_final: 0.8944 (m) REVERT: A 298 MET cc_start: 0.5076 (pmm) cc_final: 0.4695 (pmm) REVERT: A 363 SER cc_start: 0.8959 (m) cc_final: 0.8326 (t) REVERT: A 395 TYR cc_start: 0.7599 (m-80) cc_final: 0.7314 (m-80) REVERT: A 402 ASP cc_start: 0.8531 (m-30) cc_final: 0.8279 (p0) REVERT: B 181 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 189 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7849 (m90) REVERT: B 236 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8474 (mtp) REVERT: B 274 ARG cc_start: 0.9273 (tmm-80) cc_final: 0.9069 (tmm-80) REVERT: B 291 TYR cc_start: 0.7941 (t80) cc_final: 0.7138 (t80) REVERT: B 362 TYR cc_start: 0.8519 (m-80) cc_final: 0.8133 (m-80) REVERT: B 376 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8433 (ttp80) REVERT: C 192 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: C 205 ASN cc_start: 0.9043 (m-40) cc_final: 0.8671 (m110) REVERT: C 240 TYR cc_start: 0.8862 (m-80) cc_final: 0.8610 (m-80) REVERT: C 298 MET cc_start: 0.6584 (pmm) cc_final: 0.5864 (tpp) REVERT: C 406 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7180 (tm) REVERT: C 423 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (ppp) outliers start: 28 outliers final: 5 residues processed: 109 average time/residue: 0.9077 time to fit residues: 105.5242 Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.0000 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.135616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097396 restraints weight = 12742.072| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.69 r_work: 0.3464 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6291 Z= 0.210 Angle : 0.680 8.799 8460 Z= 0.342 Chirality : 0.043 0.194 969 Planarity : 0.003 0.022 1076 Dihedral : 5.196 24.934 797 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.80 % Allowed : 15.80 % Favored : 79.41 % 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: -0.95 (0.31), residues: 743 helix: 0.07 (0.24), residues: 449 sheet: -2.54 (0.82), residues: 30 loop : -1.49 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.002 0.000 HIS B 184 PHE 0.028 0.002 PHE B 306 TYR 0.016 0.002 TYR A 362 ARG 0.003 0.000 ARG B 369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8710 (m-30) cc_final: 0.8329 (t0) REVERT: A 256 CYS cc_start: 0.9185 (m) cc_final: 0.8949 (m) REVERT: A 298 MET cc_start: 0.5053 (pmm) cc_final: 0.4632 (pmm) REVERT: A 363 SER cc_start: 0.8914 (m) cc_final: 0.8297 (t) REVERT: A 395 TYR cc_start: 0.7663 (m-80) cc_final: 0.7282 (m-80) REVERT: A 402 ASP cc_start: 0.8507 (m-30) cc_final: 0.8263 (p0) REVERT: B 181 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 274 ARG cc_start: 0.9280 (tmm-80) cc_final: 0.9068 (tmm-80) REVERT: B 291 TYR cc_start: 0.7557 (t80) cc_final: 0.7052 (t80) REVERT: B 362 TYR cc_start: 0.8537 (m-80) cc_final: 0.8191 (m-80) REVERT: C 192 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: C 205 ASN cc_start: 0.9052 (m-40) cc_final: 0.8680 (m110) REVERT: C 291 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6404 (t80) REVERT: C 298 MET cc_start: 0.6460 (pmm) cc_final: 0.5615 (tpp) REVERT: C 406 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7276 (tm) REVERT: C 414 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8322 (mttm) REVERT: C 423 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8307 (ppp) outliers start: 34 outliers final: 7 residues processed: 108 average time/residue: 1.0289 time to fit residues: 117.8246 Evaluate side-chains 87 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Chi-restraints excluded: chain C residue 423 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.134890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.096597 restraints weight = 12804.367| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.67 r_work: 0.3451 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6291 Z= 0.245 Angle : 0.714 10.167 8460 Z= 0.351 Chirality : 0.044 0.221 969 Planarity : 0.003 0.027 1076 Dihedral : 5.114 24.665 797 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.10 % Allowed : 18.62 % Favored : 78.28 % 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: -0.74 (0.31), residues: 743 helix: 0.20 (0.24), residues: 453 sheet: -2.33 (0.86), residues: 30 loop : -1.34 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.001 0.000 HIS A 182 PHE 0.037 0.002 PHE B 377 TYR 0.016 0.002 TYR A 362 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8706 (m-30) cc_final: 0.8350 (t0) REVERT: A 256 CYS cc_start: 0.9194 (m) cc_final: 0.8964 (m) REVERT: A 298 MET cc_start: 0.4970 (pmm) cc_final: 0.4583 (pmm) REVERT: A 363 SER cc_start: 0.8920 (m) cc_final: 0.8271 (t) REVERT: A 384 ASN cc_start: 0.8607 (m-40) cc_final: 0.8122 (OUTLIER) REVERT: A 386 THR cc_start: 0.8900 (m) cc_final: 0.8436 (p) REVERT: A 395 TYR cc_start: 0.7719 (m-80) cc_final: 0.7441 (m-80) REVERT: B 181 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8660 (mt) REVERT: B 274 ARG cc_start: 0.9294 (tmm-80) cc_final: 0.9092 (tmm-80) REVERT: B 291 TYR cc_start: 0.7477 (t80) cc_final: 0.7246 (t80) REVERT: B 362 TYR cc_start: 0.8572 (m-80) cc_final: 0.8274 (m-80) REVERT: B 395 TYR cc_start: 0.8081 (m-10) cc_final: 0.7822 (m-10) REVERT: C 174 ASN cc_start: 0.4347 (OUTLIER) cc_final: 0.3626 (t0) REVERT: C 192 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: C 231 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7787 (tp) REVERT: C 298 MET cc_start: 0.6381 (pmm) cc_final: 0.5859 (tmm) REVERT: C 406 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7271 (tm) REVERT: C 414 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8297 (mttm) outliers start: 22 outliers final: 7 residues processed: 93 average time/residue: 0.9114 time to fit residues: 90.8986 Evaluate side-chains 81 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 25 optimal weight: 0.0570 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.135714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097859 restraints weight = 12828.882| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.64 r_work: 0.3472 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6291 Z= 0.209 Angle : 0.696 9.977 8460 Z= 0.343 Chirality : 0.044 0.275 969 Planarity : 0.003 0.027 1076 Dihedral : 4.968 24.880 797 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.96 % Allowed : 19.46 % Favored : 77.57 % 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: -0.70 (0.31), residues: 743 helix: 0.22 (0.24), residues: 448 sheet: -2.29 (0.87), residues: 30 loop : -1.29 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 253 HIS 0.001 0.000 HIS A 182 PHE 0.031 0.002 PHE B 306 TYR 0.017 0.002 TYR A 362 ARG 0.004 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8711 (m-30) cc_final: 0.8352 (t0) REVERT: A 256 CYS cc_start: 0.9219 (m) cc_final: 0.8978 (m) REVERT: A 298 MET cc_start: 0.5022 (pmm) cc_final: 0.4631 (pmm) REVERT: A 363 SER cc_start: 0.8858 (m) cc_final: 0.8179 (t) REVERT: A 384 ASN cc_start: 0.8595 (m-40) cc_final: 0.8124 (OUTLIER) REVERT: A 386 THR cc_start: 0.8907 (m) cc_final: 0.8447 (p) REVERT: B 181 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 362 TYR cc_start: 0.8552 (m-80) cc_final: 0.8274 (m-80) REVERT: B 376 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8752 (ttp80) REVERT: B 395 TYR cc_start: 0.8074 (m-10) cc_final: 0.7829 (m-10) REVERT: B 423 MET cc_start: 0.9150 (mpp) cc_final: 0.8772 (tpt) REVERT: C 174 ASN cc_start: 0.4283 (OUTLIER) cc_final: 0.3549 (t0) REVERT: C 192 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: C 205 ASN cc_start: 0.9044 (m-40) cc_final: 0.8655 (m110) REVERT: C 231 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7765 (tp) REVERT: C 298 MET cc_start: 0.6271 (pmm) cc_final: 0.5858 (tmm) REVERT: C 305 LYS cc_start: 0.9237 (mttp) cc_final: 0.9003 (mptp) REVERT: C 406 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7270 (tm) REVERT: C 414 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8258 (mttm) outliers start: 21 outliers final: 8 residues processed: 96 average time/residue: 0.7937 time to fit residues: 82.2286 Evaluate side-chains 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.136312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099430 restraints weight = 12920.667| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.66 r_work: 0.3493 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6291 Z= 0.200 Angle : 0.727 11.322 8460 Z= 0.352 Chirality : 0.045 0.359 969 Planarity : 0.003 0.026 1076 Dihedral : 4.897 24.846 797 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.54 % Allowed : 20.45 % Favored : 77.01 % 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: -0.60 (0.31), residues: 743 helix: 0.33 (0.24), residues: 448 sheet: -2.25 (0.88), residues: 30 loop : -1.30 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.001 0.000 HIS B 184 PHE 0.041 0.002 PHE B 377 TYR 0.015 0.002 TYR A 362 ARG 0.002 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8670 (m-30) cc_final: 0.8366 (t0) REVERT: A 252 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: A 256 CYS cc_start: 0.9192 (m) cc_final: 0.8959 (m) REVERT: A 298 MET cc_start: 0.5003 (pmm) cc_final: 0.4608 (pmm) REVERT: A 363 SER cc_start: 0.8844 (m) cc_final: 0.8171 (t) REVERT: A 384 ASN cc_start: 0.8580 (m-40) cc_final: 0.8130 (OUTLIER) REVERT: A 386 THR cc_start: 0.8914 (m) cc_final: 0.8470 (p) REVERT: A 395 TYR cc_start: 0.7676 (m-80) cc_final: 0.7297 (m-80) REVERT: B 181 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 395 TYR cc_start: 0.8104 (m-10) cc_final: 0.7770 (m-10) REVERT: B 404 LEU cc_start: 0.8515 (tp) cc_final: 0.8246 (mm) REVERT: B 423 MET cc_start: 0.9140 (mpp) cc_final: 0.8775 (tpt) REVERT: C 174 ASN cc_start: 0.4257 (OUTLIER) cc_final: 0.3499 (t0) REVERT: C 192 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7976 (m-80) REVERT: C 205 ASN cc_start: 0.9036 (m-40) cc_final: 0.8648 (m110) REVERT: C 231 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7685 (tp) REVERT: C 298 MET cc_start: 0.6186 (pmm) cc_final: 0.5791 (tmm) REVERT: C 305 LYS cc_start: 0.9244 (mttp) cc_final: 0.8975 (mptp) REVERT: C 406 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7509 (tm) REVERT: C 414 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8257 (mttm) outliers start: 18 outliers final: 6 residues processed: 93 average time/residue: 0.8656 time to fit residues: 86.3470 Evaluate side-chains 82 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.135492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097310 restraints weight = 12976.852| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.74 r_work: 0.3485 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6291 Z= 0.222 Angle : 0.743 11.519 8460 Z= 0.364 Chirality : 0.046 0.370 969 Planarity : 0.003 0.026 1076 Dihedral : 4.814 25.119 797 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.40 % Allowed : 21.02 % Favored : 76.59 % 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 (0.31), residues: 743 helix: 0.29 (0.24), residues: 453 sheet: -2.07 (0.90), residues: 30 loop : -1.14 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 253 HIS 0.001 0.000 HIS B 184 PHE 0.040 0.002 PHE B 306 TYR 0.014 0.002 TYR A 362 ARG 0.002 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8690 (m-30) cc_final: 0.8380 (t0) REVERT: A 256 CYS cc_start: 0.9183 (m) cc_final: 0.8942 (m) REVERT: A 298 MET cc_start: 0.5163 (pmm) cc_final: 0.4694 (pmm) REVERT: A 363 SER cc_start: 0.8837 (m) cc_final: 0.8147 (t) REVERT: A 384 ASN cc_start: 0.8643 (m-40) cc_final: 0.8202 (OUTLIER) REVERT: A 386 THR cc_start: 0.8930 (m) cc_final: 0.8518 (p) REVERT: B 181 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8703 (mt) REVERT: B 395 TYR cc_start: 0.8189 (m-10) cc_final: 0.7830 (m-10) REVERT: B 404 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8292 (mm) REVERT: B 423 MET cc_start: 0.9200 (mpp) cc_final: 0.8810 (tpt) REVERT: C 174 ASN cc_start: 0.4193 (OUTLIER) cc_final: 0.3432 (t0) REVERT: C 205 ASN cc_start: 0.9049 (m-40) cc_final: 0.8653 (m110) REVERT: C 231 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7760 (tp) REVERT: C 298 MET cc_start: 0.6078 (pmm) cc_final: 0.5701 (tmm) REVERT: C 406 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7525 (tm) REVERT: C 414 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8252 (mttm) outliers start: 17 outliers final: 6 residues processed: 87 average time/residue: 0.8566 time to fit residues: 80.0128 Evaluate side-chains 83 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 34 optimal weight: 0.0020 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.137138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.100023 restraints weight = 13046.487| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.68 r_work: 0.3508 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6291 Z= 0.199 Angle : 0.767 12.611 8460 Z= 0.367 Chirality : 0.045 0.334 969 Planarity : 0.003 0.023 1076 Dihedral : 4.724 24.559 797 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.69 % Allowed : 21.58 % Favored : 76.73 % 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: -0.42 (0.31), residues: 743 helix: 0.43 (0.25), residues: 447 sheet: -1.94 (0.93), residues: 30 loop : -1.18 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 253 HIS 0.001 0.000 HIS B 184 PHE 0.044 0.002 PHE B 306 TYR 0.012 0.002 TYR A 362 ARG 0.002 0.000 ARG B 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8660 (m-30) cc_final: 0.8355 (t0) REVERT: A 240 TYR cc_start: 0.8511 (m-80) cc_final: 0.8278 (m-80) REVERT: A 256 CYS cc_start: 0.9195 (m) cc_final: 0.8956 (m) REVERT: A 298 MET cc_start: 0.5048 (pmm) cc_final: 0.4622 (pmm) REVERT: A 363 SER cc_start: 0.8788 (m) cc_final: 0.8107 (t) REVERT: A 384 ASN cc_start: 0.8602 (m-40) cc_final: 0.8185 (p0) REVERT: A 386 THR cc_start: 0.8882 (m) cc_final: 0.8476 (p) REVERT: A 395 TYR cc_start: 0.7585 (m-80) cc_final: 0.7236 (m-80) REVERT: B 181 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8677 (mt) REVERT: B 362 TYR cc_start: 0.8431 (m-80) cc_final: 0.8169 (m-80) REVERT: B 395 TYR cc_start: 0.8167 (m-10) cc_final: 0.7866 (m-10) REVERT: B 423 MET cc_start: 0.9184 (mpp) cc_final: 0.8812 (tpt) REVERT: C 174 ASN cc_start: 0.4239 (OUTLIER) cc_final: 0.3475 (t0) REVERT: C 192 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8011 (m-80) REVERT: C 205 ASN cc_start: 0.9049 (m-40) cc_final: 0.8655 (m110) REVERT: C 231 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7675 (tp) REVERT: C 236 MET cc_start: 0.8793 (mmm) cc_final: 0.8436 (mmm) REVERT: C 298 MET cc_start: 0.5845 (pmm) cc_final: 0.5487 (tmm) REVERT: C 406 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7493 (tm) REVERT: C 414 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (mttm) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.8653 time to fit residues: 77.1745 Evaluate side-chains 84 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.099244 restraints weight = 12953.759| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.66 r_work: 0.3488 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6291 Z= 0.232 Angle : 0.765 12.375 8460 Z= 0.371 Chirality : 0.045 0.327 969 Planarity : 0.003 0.024 1076 Dihedral : 4.717 24.241 797 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.97 % Allowed : 21.44 % Favored : 76.59 % 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: -0.35 (0.31), residues: 743 helix: 0.39 (0.24), residues: 454 sheet: -1.87 (0.94), residues: 30 loop : -1.00 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 253 HIS 0.001 0.000 HIS A 182 PHE 0.045 0.002 PHE B 306 TYR 0.015 0.002 TYR A 362 ARG 0.002 0.000 ARG B 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.09 seconds wall clock time: 83 minutes 32.67 seconds (5012.67 seconds total)