Starting phenix.real_space_refine on Wed Sep 17 06:37:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yho_39290/09_2025/8yho_39290.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yho_39290/09_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_39290/09_2025/8yho_39290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yho_39290/09_2025/8yho_39290.map" model { file = "/net/cci-nas-00/data/ceres_data/8yho_39290/09_2025/8yho_39290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yho_39290/09_2025/8yho_39290.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.26 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: 0.46 Conformation dependent library (CDL) restraints added in 357.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 0.83 Time building geometry restraints manager: 0.63 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: 3.080 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.950 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- 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= 0.815 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 : 13.43 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.003 ARG C 360 TYR 0.032 0.005 TYR B 240 PHE 0.059 0.005 PHE B 377 TRP 0.024 0.005 TRP A 253 HIS 0.014 0.002 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.01792 ( 6291) covalent geometry : angle 1.52251 ( 8460) hydrogen bonds : bond 0.27660 ( 265) hydrogen bonds : angle 9.83133 ( 786) *********************** 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 : 0.269 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: 0.7962 (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: 0.8490 (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: 0.5703 time to fit residues: 83.3898 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 : 0.192 ------------------------------------------------------------------------------- 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 49 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.133849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094912 restraints weight = 12852.306| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.73 r_work: 0.3374 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6291 Z= 0.187 Angle : 0.759 9.179 8460 Z= 0.399 Chirality : 0.045 0.228 969 Planarity : 0.004 0.024 1076 Dihedral : 7.154 45.135 803 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.79 % Favored : 93.94 % Rotamer: Outliers : 3.24 % Allowed : 12.41 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.27), residues: 743 helix: -1.62 (0.21), residues: 432 sheet: -3.40 (0.68), residues: 30 loop : -2.28 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 274 TYR 0.025 0.002 TYR A 291 PHE 0.025 0.002 PHE B 306 TRP 0.024 0.003 TRP A 253 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6291) covalent geometry : angle 0.75861 ( 8460) hydrogen bonds : bond 0.04495 ( 265) hydrogen bonds : angle 5.49552 ( 786) *********************** 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 127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.153 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: 0.8759 (m-30) cc_final: 0.8326 (t0) REVERT: A 256 CYS cc_start: 0.9180 (m) cc_final: 0.8932 (m) REVERT: A 395 TYR cc_start: 0.7693 (m-80) cc_final: 0.7286 (m-80) REVERT: A 411 PHE cc_start: 0.8776 (t80) cc_final: 0.8491 (t80) REVERT: B 189 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7672 (m90) REVERT: B 263 TYR cc_start: 0.8641 (t80) cc_final: 0.8329 (t80) REVERT: B 274 ARG cc_start: 0.9158 (ttp-110) cc_final: 0.8802 (ptm-80) REVERT: B 291 TYR cc_start: 0.8098 (t80) cc_final: 0.7556 (t80) REVERT: C 406 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7477 (tm) outliers start: 23 outliers final: 3 residues processed: 119 average time/residue: 0.4196 time to fit residues: 52.6509 Evaluate side-chains 81 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 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 70 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.133995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.095238 restraints weight = 12684.462| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 3.68 r_work: 0.3366 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6291 Z= 0.161 Angle : 0.721 10.330 8460 Z= 0.366 Chirality : 0.044 0.195 969 Planarity : 0.003 0.021 1076 Dihedral : 6.040 31.138 797 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.86 % Favored : 93.00 % Rotamer: Outliers : 2.96 % Allowed : 13.96 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.29), residues: 743 helix: -0.68 (0.24), residues: 437 sheet: -3.02 (0.73), residues: 30 loop : -1.77 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 274 TYR 0.017 0.002 TYR A 362 PHE 0.024 0.002 PHE B 306 TRP 0.014 0.002 TRP A 253 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6291) covalent geometry : angle 0.72146 ( 8460) hydrogen bonds : bond 0.03625 ( 265) hydrogen bonds : angle 4.95373 ( 786) *********************** 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 120 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.235 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: 0.8721 (m-30) cc_final: 0.8309 (t0) REVERT: A 239 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7864 (ttmm) REVERT: A 256 CYS cc_start: 0.9187 (m) cc_final: 0.8948 (m) REVERT: A 290 LYS cc_start: 0.9343 (tppt) cc_final: 0.8951 (tmmt) REVERT: A 363 SER cc_start: 0.8972 (m) cc_final: 0.8345 (t) REVERT: A 395 TYR cc_start: 0.7620 (m-80) cc_final: 0.7287 (m-80) REVERT: A 402 ASP cc_start: 0.8627 (m-30) cc_final: 0.8313 (p0) REVERT: A 411 PHE cc_start: 0.8759 (t80) cc_final: 0.8386 (t80) REVERT: B 189 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7829 (m90) REVERT: B 263 TYR cc_start: 0.8565 (t80) cc_final: 0.8334 (t80) REVERT: B 291 TYR cc_start: 0.7984 (t80) cc_final: 0.7329 (t80) REVERT: B 408 PHE cc_start: 0.8487 (t80) cc_final: 0.8252 (t80) REVERT: C 192 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: C 205 ASN cc_start: 0.9050 (m-40) cc_final: 0.8678 (m110) REVERT: C 298 MET cc_start: 0.6777 (pmm) cc_final: 0.6179 (tpp) REVERT: C 305 LYS cc_start: 0.9342 (mmtm) cc_final: 0.9090 (mmtm) REVERT: C 406 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7346 (tm) REVERT: C 414 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8005 (mttt) outliers start: 21 outliers final: 5 residues processed: 113 average time/residue: 0.4425 time to fit residues: 52.8422 Evaluate side-chains 87 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain B residue 189 HIS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 414 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.134354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.096239 restraints weight = 12792.221| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.65 r_work: 0.3426 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4107 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= 0.173 Angle : 0.721 15.222 8460 Z= 0.360 Chirality : 0.044 0.220 969 Planarity : 0.003 0.021 1076 Dihedral : 5.625 29.060 797 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.65 % Allowed : 14.10 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.30), residues: 743 helix: -0.22 (0.24), residues: 447 sheet: -2.82 (0.77), residues: 30 loop : -1.65 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 274 TYR 0.017 0.002 TYR A 362 PHE 0.033 0.002 PHE B 377 TRP 0.010 0.002 TRP A 253 HIS 0.002 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6291) covalent geometry : angle 0.72105 ( 8460) hydrogen bonds : bond 0.03545 ( 265) hydrogen bonds : angle 4.77562 ( 786) *********************** 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 119 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.248 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: 0.8733 (m-30) cc_final: 0.8338 (t0) REVERT: A 239 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7690 (ptmm) REVERT: A 256 CYS cc_start: 0.9161 (m) cc_final: 0.8914 (m) REVERT: A 290 LYS cc_start: 0.9386 (tppt) cc_final: 0.9019 (tmmt) REVERT: A 363 SER cc_start: 0.9014 (m) cc_final: 0.8369 (t) REVERT: A 395 TYR cc_start: 0.7650 (m-80) cc_final: 0.7370 (m-80) REVERT: A 402 ASP cc_start: 0.8553 (m-30) cc_final: 0.8325 (p0) REVERT: A 405 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8251 (mt) REVERT: A 411 PHE cc_start: 0.8785 (t80) cc_final: 0.8391 (t80) REVERT: B 181 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 189 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7887 (m90) REVERT: B 236 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8636 (mtm) REVERT: B 263 TYR cc_start: 0.8552 (t80) cc_final: 0.8337 (t80) REVERT: B 291 TYR cc_start: 0.7954 (t80) cc_final: 0.7175 (t80) REVERT: C 192 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: C 205 ASN cc_start: 0.9063 (m-40) cc_final: 0.8681 (m110) REVERT: C 291 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.6255 (t80) REVERT: C 298 MET cc_start: 0.6970 (pmm) cc_final: 0.6414 (tpp) outliers start: 33 outliers final: 8 residues processed: 109 average time/residue: 0.4092 time to fit residues: 47.5427 Evaluate side-chains 90 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 405 LEU 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 B residue 287 ASP Chi-restraints excluded: chain B residue 404 LEU 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 313 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** C 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.135858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.097981 restraints weight = 13004.047| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.66 r_work: 0.3456 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6291 Z= 0.146 Angle : 0.720 15.685 8460 Z= 0.353 Chirality : 0.044 0.251 969 Planarity : 0.003 0.024 1076 Dihedral : 5.364 26.235 797 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.09 % Allowed : 15.37 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.31), residues: 743 helix: 0.14 (0.25), residues: 443 sheet: -2.62 (0.80), residues: 30 loop : -1.61 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 274 TYR 0.016 0.002 TYR A 362 PHE 0.030 0.002 PHE B 377 TRP 0.009 0.002 TRP A 253 HIS 0.002 0.000 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6291) covalent geometry : angle 0.72007 ( 8460) hydrogen bonds : bond 0.03356 ( 265) hydrogen bonds : angle 4.65004 ( 786) *********************** 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 115 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8708 (m-30) cc_final: 0.8327 (t0) REVERT: A 239 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7578 (ttmm) REVERT: A 256 CYS cc_start: 0.9178 (m) cc_final: 0.8937 (m) REVERT: A 290 LYS cc_start: 0.9385 (tppt) cc_final: 0.9011 (tmmt) REVERT: A 291 TYR cc_start: 0.7731 (t80) cc_final: 0.7477 (t80) REVERT: A 363 SER cc_start: 0.8925 (m) cc_final: 0.8310 (t) REVERT: A 384 ASN cc_start: 0.8581 (m-40) cc_final: 0.8086 (OUTLIER) REVERT: A 395 TYR cc_start: 0.7688 (m-80) cc_final: 0.7386 (m-80) REVERT: A 411 PHE cc_start: 0.8782 (t80) cc_final: 0.8348 (t80) REVERT: B 181 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8645 (mt) REVERT: B 291 TYR cc_start: 0.7896 (t80) cc_final: 0.7093 (t80) REVERT: B 307 ILE cc_start: 0.8742 (mt) cc_final: 0.8383 (mt) REVERT: B 376 ARG cc_start: 0.8902 (ttp80) cc_final: 0.8544 (ttp80) REVERT: B 377 PHE cc_start: 0.8440 (m-10) cc_final: 0.8134 (m-10) REVERT: C 192 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 205 ASN cc_start: 0.9060 (m-40) cc_final: 0.8674 (m110) REVERT: C 236 MET cc_start: 0.8688 (mmm) cc_final: 0.8333 (mmm) REVERT: C 291 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.6105 (t80) REVERT: C 298 MET cc_start: 0.6751 (pmm) cc_final: 0.6287 (tpp) REVERT: C 305 LYS cc_start: 0.9391 (mmtm) cc_final: 0.9121 (mptp) REVERT: C 406 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7309 (tm) outliers start: 29 outliers final: 7 residues processed: 104 average time/residue: 0.4437 time to fit residues: 48.7638 Evaluate side-chains 89 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 LYS 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 313 VAL Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.0050 chunk 54 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.4972 ------------------------------------------------------------------------------- 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 ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.136770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.098773 restraints weight = 12819.823| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.67 r_work: 0.3496 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4635 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= 0.137 Angle : 0.708 16.872 8460 Z= 0.346 Chirality : 0.043 0.253 969 Planarity : 0.003 0.030 1076 Dihedral : 5.119 25.751 797 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.10 % Allowed : 17.91 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.31), residues: 743 helix: 0.26 (0.25), residues: 449 sheet: -2.37 (0.85), residues: 30 loop : -1.44 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 274 TYR 0.015 0.002 TYR A 362 PHE 0.024 0.001 PHE B 306 TRP 0.006 0.001 TRP A 253 HIS 0.001 0.000 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6291) covalent geometry : angle 0.70778 ( 8460) hydrogen bonds : bond 0.03291 ( 265) hydrogen bonds : angle 4.60455 ( 786) *********************** 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 101 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.202 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: 0.8713 (m-30) cc_final: 0.8332 (t0) REVERT: A 256 CYS cc_start: 0.9190 (m) cc_final: 0.8938 (m) REVERT: A 290 LYS cc_start: 0.9400 (tppt) cc_final: 0.9118 (tmmt) REVERT: A 363 SER cc_start: 0.8872 (m) cc_final: 0.8269 (t) REVERT: A 384 ASN cc_start: 0.8574 (m-40) cc_final: 0.8104 (OUTLIER) REVERT: A 386 THR cc_start: 0.8860 (m) cc_final: 0.8380 (p) REVERT: A 395 TYR cc_start: 0.7760 (m-80) cc_final: 0.7520 (m-80) REVERT: B 181 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 236 MET cc_start: 0.8585 (mtm) cc_final: 0.8338 (mmm) REVERT: B 291 TYR cc_start: 0.7490 (t80) cc_final: 0.7035 (t80) REVERT: C 192 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: C 205 ASN cc_start: 0.9047 (m-40) cc_final: 0.8657 (m110) REVERT: C 236 MET cc_start: 0.8695 (mmm) cc_final: 0.8418 (mmm) REVERT: C 298 MET cc_start: 0.6564 (pmm) cc_final: 0.5955 (tpp) REVERT: C 406 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7258 (tm) outliers start: 22 outliers final: 7 residues processed: 95 average time/residue: 0.3942 time to fit residues: 40.0587 Evaluate side-chains 79 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 ASP 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 192 TYR Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.131758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092810 restraints weight = 12709.008| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.63 r_work: 0.3319 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6291 Z= 0.227 Angle : 0.775 17.531 8460 Z= 0.375 Chirality : 0.046 0.301 969 Planarity : 0.003 0.029 1076 Dihedral : 5.166 24.502 797 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.37 % Allowed : 17.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.31), residues: 743 helix: 0.25 (0.25), residues: 443 sheet: -2.29 (0.86), residues: 30 loop : -1.32 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 274 TYR 0.018 0.002 TYR A 362 PHE 0.026 0.002 PHE B 306 TRP 0.005 0.001 TRP A 253 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 6291) covalent geometry : angle 0.77511 ( 8460) hydrogen bonds : bond 0.03640 ( 265) hydrogen bonds : angle 4.76983 ( 786) *********************** 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 105 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.247 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: symmetry clash REVERT: A 206 ASP cc_start: 0.8722 (m-30) cc_final: 0.8390 (t0) REVERT: A 252 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: A 256 CYS cc_start: 0.9191 (m) cc_final: 0.8935 (m) REVERT: A 363 SER cc_start: 0.9027 (m) cc_final: 0.8396 (t) REVERT: A 384 ASN cc_start: 0.8719 (m-40) cc_final: 0.8259 (OUTLIER) REVERT: A 386 THR cc_start: 0.8908 (m) cc_final: 0.8437 (p) REVERT: B 181 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 395 TYR cc_start: 0.8197 (m-10) cc_final: 0.7946 (m-10) REVERT: C 174 ASN cc_start: 0.4309 (OUTLIER) cc_final: 0.3568 (t0) REVERT: C 236 MET cc_start: 0.8802 (mmm) cc_final: 0.8307 (mmm) REVERT: C 298 MET cc_start: 0.6585 (pmm) cc_final: 0.5815 (tpp) REVERT: C 406 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7623 (tm) outliers start: 31 outliers final: 8 residues processed: 95 average time/residue: 0.3860 time to fit residues: 39.1257 Evaluate side-chains 75 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 252 GLU 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 279 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.135827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.099249 restraints weight = 13011.533| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.62 r_work: 0.3488 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6291 Z= 0.138 Angle : 0.764 18.027 8460 Z= 0.362 Chirality : 0.044 0.279 969 Planarity : 0.003 0.027 1076 Dihedral : 4.965 25.959 797 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.40 % Allowed : 20.45 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.31), residues: 743 helix: 0.27 (0.24), residues: 443 sheet: -2.24 (0.88), residues: 30 loop : -1.31 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 376 TYR 0.017 0.002 TYR A 257 PHE 0.029 0.001 PHE B 306 TRP 0.010 0.002 TRP A 253 HIS 0.001 0.000 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6291) covalent geometry : angle 0.76450 ( 8460) hydrogen bonds : bond 0.03306 ( 265) hydrogen bonds : angle 4.68855 ( 786) *********************** 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 97 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.256 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: 0.8732 (m-30) cc_final: 0.8412 (t0) REVERT: A 256 CYS cc_start: 0.9210 (m) cc_final: 0.8971 (m) REVERT: A 363 SER cc_start: 0.8869 (m) cc_final: 0.8252 (t) REVERT: A 384 ASN cc_start: 0.8626 (m-40) cc_final: 0.8193 (OUTLIER) REVERT: A 386 THR cc_start: 0.8900 (m) cc_final: 0.8448 (p) REVERT: A 395 TYR cc_start: 0.7696 (m-80) cc_final: 0.7379 (m-80) REVERT: B 181 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8684 (mt) REVERT: B 376 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8234 (ttp80) REVERT: B 395 TYR cc_start: 0.8010 (m-10) cc_final: 0.7800 (m-10) REVERT: B 423 MET cc_start: 0.9126 (mpp) cc_final: 0.8765 (tpt) REVERT: C 174 ASN cc_start: 0.4259 (OUTLIER) cc_final: 0.3534 (t0) REVERT: C 205 ASN cc_start: 0.9031 (m-40) cc_final: 0.8626 (m110) REVERT: C 298 MET cc_start: 0.6325 (pmm) cc_final: 0.5897 (tmm) REVERT: C 406 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7495 (tm) outliers start: 17 outliers final: 8 residues processed: 93 average time/residue: 0.3693 time to fit residues: 36.9176 Evaluate side-chains 77 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 A residue 313 VAL 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 279 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 406 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 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 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 ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.136116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099823 restraints weight = 13001.527| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.62 r_work: 0.3472 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5006 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= 0.147 Angle : 0.773 18.129 8460 Z= 0.368 Chirality : 0.044 0.299 969 Planarity : 0.003 0.047 1076 Dihedral : 4.851 24.346 797 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.12 % Allowed : 20.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.31), residues: 743 helix: 0.19 (0.24), residues: 454 sheet: -2.01 (0.90), residues: 30 loop : -1.18 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 274 TYR 0.016 0.002 TYR A 291 PHE 0.035 0.001 PHE B 306 TRP 0.006 0.001 TRP A 253 HIS 0.001 0.000 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6291) covalent geometry : angle 0.77301 ( 8460) hydrogen bonds : bond 0.03297 ( 265) hydrogen bonds : angle 4.67872 ( 786) *********************** 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 93 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.262 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: 0.8714 (m-30) cc_final: 0.8405 (t0) REVERT: A 240 TYR cc_start: 0.8706 (m-80) cc_final: 0.8495 (m-80) REVERT: A 256 CYS cc_start: 0.9206 (m) cc_final: 0.8961 (m) REVERT: A 363 SER cc_start: 0.8832 (m) cc_final: 0.8136 (t) REVERT: A 384 ASN cc_start: 0.8641 (m-40) cc_final: 0.8245 (OUTLIER) REVERT: A 386 THR cc_start: 0.8919 (m) cc_final: 0.8477 (p) REVERT: A 395 TYR cc_start: 0.7652 (m-80) cc_final: 0.7389 (m-80) REVERT: B 181 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 423 MET cc_start: 0.9155 (mpp) cc_final: 0.8789 (tpt) REVERT: C 174 ASN cc_start: 0.4230 (OUTLIER) cc_final: 0.3508 (t0) REVERT: C 192 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: C 205 ASN cc_start: 0.9033 (m-40) cc_final: 0.8626 (m110) REVERT: C 231 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7585 (tp) REVERT: C 298 MET cc_start: 0.5994 (pmm) cc_final: 0.5658 (tmm) REVERT: C 406 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7511 (tm) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.3528 time to fit residues: 33.4566 Evaluate side-chains 83 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 313 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.136160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098249 restraints weight = 12920.448| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.70 r_work: 0.3453 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.5080 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= 0.155 Angle : 0.787 18.663 8460 Z= 0.376 Chirality : 0.045 0.310 969 Planarity : 0.003 0.054 1076 Dihedral : 4.861 24.554 797 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.40 % Allowed : 21.44 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.31), residues: 743 helix: 0.21 (0.24), residues: 455 sheet: -1.90 (0.92), residues: 30 loop : -1.11 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 376 TYR 0.014 0.002 TYR A 257 PHE 0.043 0.002 PHE B 306 TRP 0.005 0.001 TRP A 253 HIS 0.002 0.000 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6291) covalent geometry : angle 0.78695 ( 8460) hydrogen bonds : bond 0.03370 ( 265) hydrogen bonds : angle 4.69089 ( 786) ********************** 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 92 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.205 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: 0.8698 (m-30) cc_final: 0.8389 (t0) REVERT: A 256 CYS cc_start: 0.9194 (m) cc_final: 0.8951 (m) REVERT: A 363 SER cc_start: 0.8821 (m) cc_final: 0.8125 (t) REVERT: A 384 ASN cc_start: 0.8656 (m-40) cc_final: 0.8264 (p0) REVERT: A 386 THR cc_start: 0.8920 (m) cc_final: 0.8497 (p) REVERT: A 395 TYR cc_start: 0.7674 (m-80) cc_final: 0.7396 (m-80) REVERT: A 411 PHE cc_start: 0.8815 (t80) cc_final: 0.8604 (t80) REVERT: B 181 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 395 TYR cc_start: 0.8088 (m-10) cc_final: 0.7821 (m-10) REVERT: B 423 MET cc_start: 0.9184 (mpp) cc_final: 0.8800 (tpt) REVERT: C 174 ASN cc_start: 0.4160 (OUTLIER) cc_final: 0.3421 (t0) REVERT: C 192 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: C 205 ASN cc_start: 0.9029 (m-40) cc_final: 0.8618 (m110) REVERT: C 231 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7624 (tp) REVERT: C 298 MET cc_start: 0.5910 (pmm) cc_final: 0.5579 (tmm) REVERT: C 406 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7538 (tm) outliers start: 17 outliers final: 6 residues processed: 89 average time/residue: 0.3064 time to fit residues: 29.4754 Evaluate side-chains 81 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 347 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.135421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.098043 restraints weight = 12953.127| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.66 r_work: 0.3448 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6291 Z= 0.172 Angle : 0.823 18.133 8460 Z= 0.392 Chirality : 0.046 0.324 969 Planarity : 0.003 0.048 1076 Dihedral : 4.893 24.253 797 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.26 % Allowed : 21.58 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.31), residues: 743 helix: 0.21 (0.24), residues: 455 sheet: -1.95 (0.92), residues: 30 loop : -1.05 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 274 TYR 0.015 0.002 TYR C 240 PHE 0.050 0.002 PHE B 377 TRP 0.005 0.001 TRP A 253 HIS 0.001 0.000 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6291) covalent geometry : angle 0.82346 ( 8460) hydrogen bonds : bond 0.03393 ( 265) hydrogen bonds : angle 4.71132 ( 786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.07 seconds wall clock time: 39 minutes 16.22 seconds (2356.22 seconds total)