Starting phenix.real_space_refine on Tue Jan 14 23:37:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ur6_42484/01_2025/8ur6_42484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ur6_42484/01_2025/8ur6_42484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ur6_42484/01_2025/8ur6_42484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ur6_42484/01_2025/8ur6_42484.map" model { file = "/net/cci-nas-00/data/ceres_data/8ur6_42484/01_2025/8ur6_42484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ur6_42484/01_2025/8ur6_42484.cif" } resolution = 3.03 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= 0.022 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 36 5.16 5 C 4826 2.51 5 N 1214 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7540 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3770 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 19, 'TRANS': 445} Chain breaks: 5 Chain: "B" Number of atoms: 3770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3770 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 19, 'TRANS': 445} Chain breaks: 5 Time building chain proxies: 5.02, per 1000 atoms: 0.67 Number of scatterers: 7540 At special positions: 0 Unit cell: (103.356, 115.884, 72.036, 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 36 16.00 O 1464 8.00 N 1214 7.00 C 4826 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: 1.68 Conformation dependent library (CDL) restraints added in 977.3 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 8 sheets defined 40.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 3.638A pdb=" N PHE A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 157 through 162 removed outlier: 4.056A pdb=" N ASP A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.524A pdb=" N PHE A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.511A pdb=" N ARG A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.862A pdb=" N GLY A 330 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.911A pdb=" N ILE A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 449 through 457 removed outlier: 3.734A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 524 Processing helix chain 'B' and resid 6 through 11 removed outlier: 3.647A pdb=" N PHE B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 158 through 162 removed outlier: 4.024A pdb=" N ASP B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.612A pdb=" N PHE B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 313 through 326 removed outlier: 3.865A pdb=" N GLN B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.772A pdb=" N GLY B 330 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.551A pdb=" N GLN B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 365 removed outlier: 3.830A pdb=" N ILE B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.642A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 524 removed outlier: 3.505A pdb=" N SER B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.378A pdb=" N ILE A 52 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU A 245 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE A 54 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER A 24 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N PHE A 287 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR A 26 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.316A pdb=" N MET A 389 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 413 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N VAL A 346 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257 removed outlier: 5.594A pdb=" N VAL A 250 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP A 270 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 256 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA A 264 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.500A pdb=" N SER B 24 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N PHE B 287 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR B 26 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR B 289 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 28 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133 removed outlier: 4.309A pdb=" N MET B 389 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA B 413 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL B 346 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.756A pdb=" N VAL B 248 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG B 271 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 250 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 269 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 252 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 267 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS B 254 " --> pdb=" O ARG B 265 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2408 1.34 - 1.47: 1940 1.47 - 1.59: 3312 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 7718 Sorted by residual: bond pdb=" CA ILE B 461 " pdb=" C ILE B 461 " ideal model delta sigma weight residual 1.528 1.495 0.033 8.50e-03 1.38e+04 1.49e+01 bond pdb=" N ILE B 461 " pdb=" CA ILE B 461 " ideal model delta sigma weight residual 1.458 1.483 -0.026 7.70e-03 1.69e+04 1.10e+01 bond pdb=" N PRO A 462 " pdb=" CD PRO A 462 " ideal model delta sigma weight residual 1.473 1.505 -0.032 1.40e-02 5.10e+03 5.31e+00 bond pdb=" CA GLU B 190 " pdb=" C GLU B 190 " ideal model delta sigma weight residual 1.520 1.538 -0.017 1.02e-02 9.61e+03 2.90e+00 bond pdb=" CA GLU A 190 " pdb=" C GLU A 190 " ideal model delta sigma weight residual 1.520 1.535 -0.015 9.90e-03 1.02e+04 2.25e+00 ... (remaining 7713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 9866 1.49 - 2.99: 549 2.99 - 4.48: 57 4.48 - 5.98: 4 5.98 - 7.47: 2 Bond angle restraints: 10478 Sorted by residual: angle pdb=" C LYS A 184 " pdb=" N THR A 185 " pdb=" CA THR A 185 " ideal model delta sigma weight residual 122.09 117.49 4.60 1.79e+00 3.12e-01 6.60e+00 angle pdb=" CA TYR B 236 " pdb=" CB TYR B 236 " pdb=" CG TYR B 236 " ideal model delta sigma weight residual 113.90 117.97 -4.07 1.80e+00 3.09e-01 5.10e+00 angle pdb=" C GLU A 501 " pdb=" N ARG A 502 " pdb=" CA ARG A 502 " ideal model delta sigma weight residual 122.19 125.26 -3.07 1.41e+00 5.03e-01 4.73e+00 angle pdb=" CA VAL B 169 " pdb=" C VAL B 169 " pdb=" N PHE B 170 " ideal model delta sigma weight residual 116.60 119.68 -3.08 1.45e+00 4.76e-01 4.52e+00 angle pdb=" C ILE A 255 " pdb=" N ASP A 256 " pdb=" CA ASP A 256 " ideal model delta sigma weight residual 123.00 120.07 2.93 1.38e+00 5.25e-01 4.50e+00 ... (remaining 10473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 4078 15.65 - 31.30: 383 31.30 - 46.95: 92 46.95 - 62.60: 21 62.60 - 78.25: 6 Dihedral angle restraints: 4580 sinusoidal: 1838 harmonic: 2742 Sorted by residual: dihedral pdb=" CA VAL B 483 " pdb=" C VAL B 483 " pdb=" N VAL B 484 " pdb=" CA VAL B 484 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ILE A 255 " pdb=" C ILE A 255 " pdb=" N ASP A 256 " pdb=" CA ASP A 256 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ILE B 255 " pdb=" C ILE B 255 " pdb=" N ASP B 256 " pdb=" CA ASP B 256 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 ... (remaining 4577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 691 0.040 - 0.080: 336 0.080 - 0.120: 108 0.120 - 0.160: 19 0.160 - 0.199: 4 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CA ILE B 255 " pdb=" N ILE B 255 " pdb=" C ILE B 255 " pdb=" CB ILE B 255 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA ILE B 411 " pdb=" N ILE B 411 " pdb=" C ILE B 411 " pdb=" CB ILE B 411 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 1155 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 461 " -0.077 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO A 462 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 462 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 462 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 461 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 462 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 387 " -0.001 2.00e-02 2.50e+03 1.18e-02 3.48e+00 pdb=" CG TRP B 387 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP B 387 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 387 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 387 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 387 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP B 387 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 387 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 387 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 387 " -0.019 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1029 2.75 - 3.29: 7316 3.29 - 3.83: 12832 3.83 - 4.36: 15821 4.36 - 4.90: 26519 Nonbonded interactions: 63517 Sorted by model distance: nonbonded pdb=" OG SER A 431 " pdb=" OD1 ASN A 433 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 431 " pdb=" OD1 ASN B 433 " model vdw 2.236 3.040 nonbonded pdb=" OG SER A 347 " pdb=" NE1 TRP A 410 " model vdw 2.293 3.120 nonbonded pdb=" OG SER B 347 " pdb=" NE1 TRP B 410 " model vdw 2.294 3.120 nonbonded pdb=" O THR B 185 " pdb=" OH TYR B 412 " model vdw 2.297 3.040 ... (remaining 63512 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 20.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.007 0.052 7718 Z= 0.439 Angle : 0.760 7.474 10478 Z= 0.419 Chirality : 0.050 0.199 1158 Planarity : 0.007 0.119 1336 Dihedral : 13.542 78.246 2800 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -0.07 (0.26), residues: 906 helix: 0.82 (0.29), residues: 284 sheet: -0.15 (0.45), residues: 130 loop : -0.48 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP B 387 HIS 0.011 0.003 HIS A 86 PHE 0.017 0.004 PHE B 170 TYR 0.022 0.004 TYR B 236 ARG 0.014 0.003 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.934 Fit side-chains REVERT: A 51 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8463 (mmtm) REVERT: A 157 ASN cc_start: 0.8604 (m-40) cc_final: 0.8180 (p0) REVERT: A 202 LEU cc_start: 0.9582 (mp) cc_final: 0.9297 (mt) REVERT: A 268 LEU cc_start: 0.8925 (mp) cc_final: 0.8647 (mp) REVERT: A 272 ASN cc_start: 0.9197 (t0) cc_final: 0.8991 (p0) REVERT: A 274 ASN cc_start: 0.8423 (m-40) cc_final: 0.8167 (p0) REVERT: A 311 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 389 MET cc_start: 0.8892 (ttm) cc_final: 0.8661 (ttm) REVERT: A 473 MET cc_start: 0.8935 (mmm) cc_final: 0.8678 (mmm) REVERT: B 58 LEU cc_start: 0.9013 (mm) cc_final: 0.8713 (pp) REVERT: B 104 ASN cc_start: 0.9364 (m-40) cc_final: 0.9104 (m-40) REVERT: B 112 TYR cc_start: 0.8558 (t80) cc_final: 0.8019 (t80) REVERT: B 159 GLU cc_start: 0.8754 (mp0) cc_final: 0.8518 (pm20) REVERT: B 173 ASP cc_start: 0.8920 (m-30) cc_final: 0.8557 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1948 time to fit residues: 34.7326 Evaluate side-chains 75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 321 ASN B 207 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.077648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063026 restraints weight = 19003.991| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.20 r_work: 0.2834 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7718 Z= 0.264 Angle : 0.493 5.056 10478 Z= 0.271 Chirality : 0.044 0.155 1158 Planarity : 0.004 0.062 1336 Dihedral : 4.080 17.965 994 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.07 % Allowed : 4.52 % Favored : 94.40 % 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: 0.45 (0.27), residues: 906 helix: 1.31 (0.30), residues: 300 sheet: -0.10 (0.46), residues: 130 loop : -0.16 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.006 0.001 HIS A 207 PHE 0.026 0.001 PHE A 506 TYR 0.016 0.001 TYR B 236 ARG 0.005 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.941 Fit side-chains REVERT: A 157 ASN cc_start: 0.8554 (m-40) cc_final: 0.8260 (t0) REVERT: A 249 LYS cc_start: 0.8969 (tmtt) cc_final: 0.8716 (ttmm) REVERT: A 272 ASN cc_start: 0.9274 (t0) cc_final: 0.9013 (p0) REVERT: A 274 ASN cc_start: 0.8471 (m-40) cc_final: 0.8100 (p0) REVERT: A 311 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 465 MET cc_start: 0.9252 (mtm) cc_final: 0.8963 (mtt) REVERT: A 473 MET cc_start: 0.9148 (mmm) cc_final: 0.8837 (mmm) REVERT: B 58 LEU cc_start: 0.9085 (mm) cc_final: 0.8751 (pp) REVERT: B 159 GLU cc_start: 0.8926 (mp0) cc_final: 0.8547 (tp30) REVERT: B 173 ASP cc_start: 0.8969 (m-30) cc_final: 0.8548 (t0) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 0.1788 time to fit residues: 20.2935 Evaluate side-chains 67 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 321 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 = 0.3291 r_free = 0.3291 target = 0.075990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061855 restraints weight = 19209.449| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.18 r_work: 0.2801 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7718 Z= 0.267 Angle : 0.483 4.512 10478 Z= 0.265 Chirality : 0.043 0.153 1158 Planarity : 0.004 0.049 1336 Dihedral : 3.991 18.895 994 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.83 % Allowed : 6.31 % Favored : 92.86 % 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: 0.67 (0.28), residues: 906 helix: 1.37 (0.30), residues: 302 sheet: -0.14 (0.47), residues: 130 loop : 0.11 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.005 0.001 HIS B 207 PHE 0.027 0.001 PHE A 506 TYR 0.015 0.001 TYR A 236 ARG 0.004 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.930 Fit side-chains REVERT: A 157 ASN cc_start: 0.8559 (m-40) cc_final: 0.8353 (t0) REVERT: A 173 ASP cc_start: 0.8913 (m-30) cc_final: 0.8574 (t0) REVERT: A 249 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8787 (ttmm) REVERT: A 272 ASN cc_start: 0.9272 (t0) cc_final: 0.8893 (p0) REVERT: A 311 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 473 MET cc_start: 0.9124 (mmm) cc_final: 0.8834 (mmm) REVERT: B 58 LEU cc_start: 0.9143 (mm) cc_final: 0.8792 (pp) REVERT: B 157 ASN cc_start: 0.8230 (t0) cc_final: 0.7245 (t0) REVERT: B 159 GLU cc_start: 0.8847 (mp0) cc_final: 0.8297 (pm20) REVERT: B 173 ASP cc_start: 0.8922 (m-30) cc_final: 0.8520 (t0) REVERT: B 274 ASN cc_start: 0.8677 (m-40) cc_final: 0.8180 (p0) REVERT: B 506 PHE cc_start: 0.8997 (t80) cc_final: 0.8761 (t80) outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1672 time to fit residues: 17.1523 Evaluate side-chains 67 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 486 HIS B 207 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.076772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062105 restraints weight = 18808.543| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.28 r_work: 0.2825 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7718 Z= 0.173 Angle : 0.432 5.168 10478 Z= 0.237 Chirality : 0.042 0.148 1158 Planarity : 0.003 0.045 1336 Dihedral : 3.788 17.819 994 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.71 % Allowed : 7.02 % Favored : 92.26 % 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: 0.84 (0.28), residues: 906 helix: 1.49 (0.30), residues: 302 sheet: -0.11 (0.47), residues: 130 loop : 0.26 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 316 HIS 0.005 0.001 HIS A 207 PHE 0.015 0.001 PHE A 506 TYR 0.012 0.001 TYR B 236 ARG 0.002 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8940 (m-30) cc_final: 0.8585 (t0) REVERT: A 249 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8772 (ttmm) REVERT: A 272 ASN cc_start: 0.9260 (t0) cc_final: 0.8969 (p0) REVERT: A 311 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 473 MET cc_start: 0.9098 (mmm) cc_final: 0.8883 (mmm) REVERT: B 58 LEU cc_start: 0.9194 (mm) cc_final: 0.8874 (pp) REVERT: B 157 ASN cc_start: 0.8174 (t0) cc_final: 0.7397 (t0) REVERT: B 159 GLU cc_start: 0.8879 (mp0) cc_final: 0.8431 (pm20) REVERT: B 173 ASP cc_start: 0.8924 (m-30) cc_final: 0.8505 (t0) REVERT: B 272 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9030 (m-40) REVERT: B 365 CYS cc_start: 0.7798 (t) cc_final: 0.7588 (p) outliers start: 6 outliers final: 2 residues processed: 72 average time/residue: 0.1847 time to fit residues: 19.6810 Evaluate side-chains 62 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058516 restraints weight = 19153.399| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.21 r_work: 0.2754 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7718 Z= 0.294 Angle : 0.484 4.572 10478 Z= 0.267 Chirality : 0.044 0.157 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.962 17.767 994 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.83 % Allowed : 7.62 % Favored : 91.55 % 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: 0.86 (0.28), residues: 906 helix: 1.38 (0.30), residues: 302 sheet: -0.08 (0.48), residues: 130 loop : 0.37 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 316 HIS 0.006 0.001 HIS B 207 PHE 0.025 0.001 PHE A 506 TYR 0.017 0.001 TYR B 236 ARG 0.004 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8937 (m-30) cc_final: 0.8576 (t0) REVERT: A 235 GLU cc_start: 0.9097 (tp30) cc_final: 0.8854 (mm-30) REVERT: A 249 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8775 (ttmm) REVERT: A 272 ASN cc_start: 0.9341 (t0) cc_final: 0.9004 (p0) REVERT: A 311 GLU cc_start: 0.8493 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 326 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8720 (p) REVERT: A 473 MET cc_start: 0.9110 (mmm) cc_final: 0.8873 (mmm) REVERT: B 58 LEU cc_start: 0.9177 (mm) cc_final: 0.8831 (pp) REVERT: B 173 ASP cc_start: 0.8949 (m-30) cc_final: 0.8543 (t0) REVERT: B 272 ASN cc_start: 0.9356 (OUTLIER) cc_final: 0.9076 (m-40) REVERT: B 274 ASN cc_start: 0.8623 (m-40) cc_final: 0.8058 (p0) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 0.1673 time to fit residues: 16.2233 Evaluate side-chains 63 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 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 = 0.3235 r_free = 0.3235 target = 0.072901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.058610 restraints weight = 19058.288| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.26 r_work: 0.2754 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7718 Z= 0.258 Angle : 0.467 4.620 10478 Z= 0.258 Chirality : 0.043 0.143 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.917 17.565 994 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.60 % Allowed : 8.33 % Favored : 91.07 % 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: 0.87 (0.28), residues: 906 helix: 1.40 (0.30), residues: 302 sheet: -0.14 (0.48), residues: 130 loop : 0.38 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 316 HIS 0.002 0.001 HIS B 456 PHE 0.015 0.001 PHE A 506 TYR 0.016 0.001 TYR A 471 ARG 0.004 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8948 (m-30) cc_final: 0.8578 (t0) REVERT: A 249 LYS cc_start: 0.9010 (tmtt) cc_final: 0.8767 (ttmm) REVERT: A 272 ASN cc_start: 0.9358 (t0) cc_final: 0.9005 (p0) REVERT: A 311 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 473 MET cc_start: 0.9096 (mmm) cc_final: 0.8798 (mmm) REVERT: B 58 LEU cc_start: 0.9179 (mm) cc_final: 0.8824 (pp) REVERT: B 159 GLU cc_start: 0.8910 (mp0) cc_final: 0.8649 (tp30) REVERT: B 173 ASP cc_start: 0.8987 (m-30) cc_final: 0.8564 (t0) REVERT: B 272 ASN cc_start: 0.9371 (OUTLIER) cc_final: 0.9098 (m-40) REVERT: B 274 ASN cc_start: 0.8599 (m-40) cc_final: 0.8062 (p0) REVERT: B 365 CYS cc_start: 0.7823 (t) cc_final: 0.7603 (p) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.1576 time to fit residues: 14.5286 Evaluate side-chains 56 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 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 = 0.3247 r_free = 0.3247 target = 0.073559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059449 restraints weight = 18919.887| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.18 r_work: 0.2773 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7718 Z= 0.206 Angle : 0.457 4.937 10478 Z= 0.251 Chirality : 0.043 0.145 1158 Planarity : 0.003 0.042 1336 Dihedral : 3.859 16.773 994 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.71 % Allowed : 8.45 % Favored : 90.83 % 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: 0.91 (0.28), residues: 906 helix: 1.45 (0.31), residues: 302 sheet: -0.14 (0.48), residues: 130 loop : 0.40 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.005 0.001 HIS B 0 PHE 0.019 0.001 PHE A 506 TYR 0.013 0.001 TYR A 412 ARG 0.003 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.861 Fit side-chains REVERT: A 173 ASP cc_start: 0.8937 (m-30) cc_final: 0.8564 (t0) REVERT: A 249 LYS cc_start: 0.8985 (tmtt) cc_final: 0.8753 (ttmm) REVERT: A 272 ASN cc_start: 0.9334 (t0) cc_final: 0.8990 (p0) REVERT: A 311 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 326 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 389 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8058 (ttm) REVERT: A 473 MET cc_start: 0.9118 (mmm) cc_final: 0.8808 (mmm) REVERT: B 58 LEU cc_start: 0.9185 (mm) cc_final: 0.8822 (pp) REVERT: B 159 GLU cc_start: 0.8906 (mp0) cc_final: 0.8625 (tp30) REVERT: B 173 ASP cc_start: 0.8961 (m-30) cc_final: 0.8514 (t0) REVERT: B 272 ASN cc_start: 0.9377 (OUTLIER) cc_final: 0.9079 (m-40) REVERT: B 274 ASN cc_start: 0.8570 (m-40) cc_final: 0.8044 (p0) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.1608 time to fit residues: 14.7550 Evaluate side-chains 60 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 321 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 = 0.3286 r_free = 0.3286 target = 0.075542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061291 restraints weight = 19226.616| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.29 r_work: 0.2829 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7718 Z= 0.145 Angle : 0.430 6.180 10478 Z= 0.237 Chirality : 0.042 0.147 1158 Planarity : 0.003 0.041 1336 Dihedral : 3.674 15.573 994 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.60 % Allowed : 9.29 % Favored : 90.12 % 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: 1.01 (0.28), residues: 906 helix: 1.59 (0.31), residues: 302 sheet: -0.00 (0.48), residues: 130 loop : 0.39 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.006 0.001 HIS A 207 PHE 0.013 0.001 PHE A 506 TYR 0.013 0.001 TYR A 412 ARG 0.002 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.884 Fit side-chains REVERT: A 173 ASP cc_start: 0.8930 (m-30) cc_final: 0.8547 (t0) REVERT: A 249 LYS cc_start: 0.8959 (tmtt) cc_final: 0.8729 (ttmm) REVERT: A 272 ASN cc_start: 0.9346 (t0) cc_final: 0.8980 (p0) REVERT: A 311 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 326 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.8891 (p) REVERT: A 473 MET cc_start: 0.9119 (mmm) cc_final: 0.8817 (mmm) REVERT: B 58 LEU cc_start: 0.9172 (mm) cc_final: 0.8762 (pp) REVERT: B 159 GLU cc_start: 0.8956 (mp0) cc_final: 0.8598 (tp30) REVERT: B 173 ASP cc_start: 0.8968 (m-30) cc_final: 0.8509 (t0) REVERT: B 272 ASN cc_start: 0.9376 (OUTLIER) cc_final: 0.9135 (m-40) REVERT: B 274 ASN cc_start: 0.8563 (m-40) cc_final: 0.8075 (p0) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.1586 time to fit residues: 16.5791 Evaluate side-chains 58 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 272 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 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 = 0.3291 r_free = 0.3291 target = 0.076010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061594 restraints weight = 19350.548| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.35 r_work: 0.2825 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7718 Z= 0.148 Angle : 0.439 5.984 10478 Z= 0.241 Chirality : 0.042 0.144 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.683 16.122 994 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.95 % Allowed : 10.24 % Favored : 88.81 % 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: 1.02 (0.28), residues: 906 helix: 1.55 (0.30), residues: 300 sheet: 0.07 (0.48), residues: 130 loop : 0.41 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.002 0.000 HIS A 0 PHE 0.015 0.001 PHE A 506 TYR 0.012 0.001 TYR A 412 ARG 0.001 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.881 Fit side-chains REVERT: A 51 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8578 (mmtm) REVERT: A 173 ASP cc_start: 0.8931 (m-30) cc_final: 0.8556 (t0) REVERT: A 249 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8731 (ttmm) REVERT: A 272 ASN cc_start: 0.9311 (t0) cc_final: 0.8946 (p0) REVERT: A 311 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 326 SER cc_start: 0.9248 (OUTLIER) cc_final: 0.8906 (p) REVERT: A 389 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: A 473 MET cc_start: 0.9133 (mmm) cc_final: 0.8838 (mmm) REVERT: B 51 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8627 (mmtm) REVERT: B 159 GLU cc_start: 0.8948 (mp0) cc_final: 0.8634 (tp30) REVERT: B 173 ASP cc_start: 0.8950 (m-30) cc_final: 0.8497 (t0) REVERT: B 272 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.9117 (m-40) REVERT: B 274 ASN cc_start: 0.8578 (m-40) cc_final: 0.8108 (p0) REVERT: B 473 MET cc_start: 0.9042 (mmm) cc_final: 0.8815 (mmm) outliers start: 8 outliers final: 2 residues processed: 58 average time/residue: 0.1728 time to fit residues: 14.9659 Evaluate side-chains 59 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 272 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061183 restraints weight = 19138.662| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.28 r_work: 0.2826 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7718 Z= 0.168 Angle : 0.443 6.743 10478 Z= 0.244 Chirality : 0.042 0.143 1158 Planarity : 0.003 0.044 1336 Dihedral : 3.682 16.160 994 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 10.71 % Favored : 88.57 % 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: 1.04 (0.28), residues: 906 helix: 1.58 (0.31), residues: 300 sheet: 0.14 (0.48), residues: 130 loop : 0.40 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.002 0.000 HIS B 456 PHE 0.015 0.001 PHE A 506 TYR 0.013 0.001 TYR A 412 ARG 0.002 0.000 ARG A 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.971 Fit side-chains REVERT: A 51 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8557 (mmtm) REVERT: A 173 ASP cc_start: 0.8951 (m-30) cc_final: 0.8571 (t0) REVERT: A 249 LYS cc_start: 0.8953 (tmtt) cc_final: 0.8693 (ttmm) REVERT: A 272 ASN cc_start: 0.9321 (t0) cc_final: 0.8845 (p0) REVERT: A 311 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8152 (tm-30) REVERT: A 326 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.9029 (t) REVERT: A 389 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7953 (mtp) REVERT: A 473 MET cc_start: 0.9121 (mmm) cc_final: 0.8888 (mmm) REVERT: B 159 GLU cc_start: 0.8971 (mp0) cc_final: 0.8582 (tp30) REVERT: B 173 ASP cc_start: 0.8973 (m-30) cc_final: 0.8520 (t0) REVERT: B 272 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9119 (m-40) REVERT: B 274 ASN cc_start: 0.8578 (m-40) cc_final: 0.8107 (p0) REVERT: B 473 MET cc_start: 0.9056 (mmm) cc_final: 0.8831 (mmm) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1708 time to fit residues: 14.0348 Evaluate side-chains 57 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 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 = 0.3280 r_free = 0.3280 target = 0.075216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060951 restraints weight = 19009.370| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.28 r_work: 0.2817 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7718 Z= 0.182 Angle : 0.445 6.377 10478 Z= 0.245 Chirality : 0.042 0.141 1158 Planarity : 0.003 0.044 1336 Dihedral : 3.706 15.721 994 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.95 % Allowed : 10.71 % Favored : 88.33 % 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: 1.08 (0.28), residues: 906 helix: 1.58 (0.31), residues: 300 sheet: 0.17 (0.48), residues: 130 loop : 0.44 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.002 0.000 HIS B 456 PHE 0.009 0.001 PHE B 40 TYR 0.013 0.001 TYR A 412 ARG 0.002 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.72 seconds wall clock time: 58 minutes 26.29 seconds (3506.29 seconds total)