Starting phenix.real_space_refine on Sat Aug 3 08:34:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/08_2024/8ur6_42484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/08_2024/8ur6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/08_2024/8ur6_42484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/08_2024/8ur6_42484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/08_2024/8ur6_42484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/08_2024/8ur6_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 Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.42, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.87 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: 2.03 Time building geometry restraints manager: 2.92 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: 99.18 - 106.21: 176 106.21 - 113.24: 4162 113.24 - 120.26: 2868 120.26 - 127.29: 3173 127.29 - 134.32: 99 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: 0.00 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: 1.170 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.550 Find NCS groups from input model: 0.180 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.853 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: 0.1846 time to fit residues: 32.7121 Evaluate side-chains 75 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.829 Fit side-chains REVERT: A 157 ASN cc_start: 0.8495 (m-40) cc_final: 0.8196 (t0) REVERT: A 249 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8656 (ttmm) REVERT: A 272 ASN cc_start: 0.9236 (t0) cc_final: 0.8988 (p0) REVERT: A 274 ASN cc_start: 0.8431 (m-40) cc_final: 0.8031 (p0) REVERT: A 311 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 465 MET cc_start: 0.9320 (mtm) cc_final: 0.9030 (mtt) REVERT: A 473 MET cc_start: 0.9088 (mmm) cc_final: 0.8751 (mmm) REVERT: B 58 LEU cc_start: 0.9045 (mm) cc_final: 0.8677 (pp) REVERT: B 159 GLU cc_start: 0.8868 (mp0) cc_final: 0.8490 (tp30) REVERT: B 173 ASP cc_start: 0.8984 (m-30) cc_final: 0.8543 (t0) outliers start: 9 outliers final: 5 residues processed: 78 average time/residue: 0.1706 time to fit residues: 19.2203 Evaluate side-chains 67 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 46 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 0.0870 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS B 207 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7718 Z= 0.163 Angle : 0.441 4.439 10478 Z= 0.241 Chirality : 0.042 0.154 1158 Planarity : 0.003 0.048 1336 Dihedral : 3.837 17.875 994 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.60 % Allowed : 6.67 % Favored : 92.74 % 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: 0.68 (0.28), residues: 906 helix: 1.48 (0.30), residues: 302 sheet: -0.11 (0.46), residues: 130 loop : 0.04 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 316 HIS 0.005 0.001 HIS B 207 PHE 0.022 0.001 PHE A 506 TYR 0.012 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 fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.914 Fit side-chains REVERT: A 51 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8615 (mmtm) REVERT: A 173 ASP cc_start: 0.8969 (m-30) cc_final: 0.8594 (t0) REVERT: A 249 LYS cc_start: 0.8914 (tmtt) cc_final: 0.8678 (ttmm) REVERT: A 272 ASN cc_start: 0.9255 (t0) cc_final: 0.8909 (p0) REVERT: A 311 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 465 MET cc_start: 0.9305 (mtm) cc_final: 0.9019 (mtt) REVERT: A 473 MET cc_start: 0.9054 (mmm) cc_final: 0.8716 (mmm) REVERT: B 57 GLU cc_start: 0.8594 (mp0) cc_final: 0.8382 (mp0) REVERT: B 58 LEU cc_start: 0.9066 (mm) cc_final: 0.8675 (pp) REVERT: B 157 ASN cc_start: 0.8023 (t0) cc_final: 0.7434 (t0) REVERT: B 159 GLU cc_start: 0.8766 (mp0) cc_final: 0.8311 (pm20) REVERT: B 173 ASP cc_start: 0.8969 (m-30) cc_final: 0.8466 (t0) outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.1732 time to fit residues: 17.6125 Evaluate side-chains 62 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 272 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7718 Z= 0.285 Angle : 0.479 4.491 10478 Z= 0.263 Chirality : 0.043 0.147 1158 Planarity : 0.004 0.046 1336 Dihedral : 3.969 18.542 994 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.95 % Allowed : 6.55 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 906 helix: 1.47 (0.31), residues: 300 sheet: -0.14 (0.47), residues: 130 loop : 0.23 (0.28), residues: 476 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 0.021 0.001 PHE A 506 TYR 0.017 0.001 TYR B 236 ARG 0.005 0.000 ARG B 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 70 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8988 (m-30) cc_final: 0.8599 (t0) REVERT: A 249 LYS cc_start: 0.8950 (tmtt) cc_final: 0.8708 (ttmm) REVERT: A 272 ASN cc_start: 0.9304 (t0) cc_final: 0.8984 (p0) REVERT: A 311 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 473 MET cc_start: 0.9019 (mmm) cc_final: 0.8759 (mmm) REVERT: B 57 GLU cc_start: 0.8637 (mp0) cc_final: 0.8367 (mp0) REVERT: B 58 LEU cc_start: 0.9128 (mm) cc_final: 0.8753 (pp) REVERT: B 173 ASP cc_start: 0.8988 (m-30) cc_final: 0.8553 (t0) REVERT: B 448 ASP cc_start: 0.8895 (m-30) cc_final: 0.8691 (p0) REVERT: B 506 PHE cc_start: 0.8990 (t80) cc_final: 0.8692 (t80) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.1713 time to fit residues: 16.5204 Evaluate side-chains 63 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 436 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7718 Z= 0.273 Angle : 0.468 4.606 10478 Z= 0.258 Chirality : 0.043 0.150 1158 Planarity : 0.003 0.045 1336 Dihedral : 3.955 18.277 994 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 7.50 % Favored : 91.79 % 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: 1.36 (0.30), residues: 302 sheet: -0.08 (0.48), residues: 130 loop : 0.35 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.006 0.001 HIS A 207 PHE 0.024 0.001 PHE A 506 TYR 0.015 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 fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.832 Fit side-chains REVERT: A 173 ASP cc_start: 0.8994 (m-30) cc_final: 0.8599 (t0) REVERT: A 249 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8674 (ttmm) REVERT: A 272 ASN cc_start: 0.9307 (t0) cc_final: 0.8977 (p0) REVERT: A 311 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 473 MET cc_start: 0.9049 (mmm) cc_final: 0.8790 (mmm) REVERT: B 57 GLU cc_start: 0.8766 (mp0) cc_final: 0.8457 (mp0) REVERT: B 58 LEU cc_start: 0.9138 (mm) cc_final: 0.8765 (pp) REVERT: B 157 ASN cc_start: 0.8327 (t0) cc_final: 0.7309 (t0) REVERT: B 173 ASP cc_start: 0.9001 (m-30) cc_final: 0.8574 (t0) REVERT: B 272 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8964 (m-40) REVERT: B 274 ASN cc_start: 0.8571 (m-40) cc_final: 0.8006 (p0) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.1570 time to fit residues: 14.9522 Evaluate side-chains 57 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LYS 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 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7718 Z= 0.167 Angle : 0.432 4.732 10478 Z= 0.237 Chirality : 0.042 0.148 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.795 17.205 994 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.83 % Allowed : 7.50 % Favored : 91.67 % 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: 0.93 (0.28), residues: 906 helix: 1.46 (0.30), residues: 302 sheet: -0.01 (0.49), residues: 130 loop : 0.37 (0.28), 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 0.019 0.001 PHE B 506 TYR 0.014 0.001 TYR B 412 ARG 0.002 0.000 ARG B 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 65 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.853 Fit side-chains REVERT: A 173 ASP cc_start: 0.8974 (m-30) cc_final: 0.8575 (t0) REVERT: A 249 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8684 (ttmm) REVERT: A 272 ASN cc_start: 0.9272 (t0) cc_final: 0.8958 (p0) REVERT: A 311 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7883 (tm-30) REVERT: A 326 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 473 MET cc_start: 0.9053 (mmm) cc_final: 0.8719 (mmm) REVERT: B 57 GLU cc_start: 0.8757 (mp0) cc_final: 0.8468 (mp0) REVERT: B 58 LEU cc_start: 0.9175 (mm) cc_final: 0.8799 (pp) REVERT: B 173 ASP cc_start: 0.8997 (m-30) cc_final: 0.8553 (t0) REVERT: B 272 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8943 (m-40) REVERT: B 274 ASN cc_start: 0.8523 (m-40) cc_final: 0.8014 (p0) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.1577 time to fit residues: 14.8969 Evaluate side-chains 58 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7718 Z= 0.201 Angle : 0.444 4.657 10478 Z= 0.244 Chirality : 0.043 0.144 1158 Planarity : 0.003 0.045 1336 Dihedral : 3.834 16.499 994 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 8.69 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 906 helix: 1.48 (0.30), residues: 302 sheet: -0.02 (0.48), residues: 130 loop : 0.40 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 316 HIS 0.003 0.001 HIS B 0 PHE 0.021 0.001 PHE B 506 TYR 0.014 0.001 TYR A 412 ARG 0.003 0.000 ARG B 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 fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8979 (m-30) cc_final: 0.8579 (t0) REVERT: A 249 LYS cc_start: 0.8910 (tmtt) cc_final: 0.8682 (ttmm) REVERT: A 272 ASN cc_start: 0.9280 (t0) cc_final: 0.8954 (p0) REVERT: A 311 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 326 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8707 (t) REVERT: A 473 MET cc_start: 0.9072 (mmm) cc_final: 0.8737 (mmm) REVERT: B 57 GLU cc_start: 0.8759 (mp0) cc_final: 0.8469 (mp0) REVERT: B 58 LEU cc_start: 0.9191 (mm) cc_final: 0.8800 (pp) REVERT: B 173 ASP cc_start: 0.9027 (m-30) cc_final: 0.8571 (t0) REVERT: B 272 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8962 (m-40) REVERT: B 274 ASN cc_start: 0.8533 (m-40) cc_final: 0.8020 (p0) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.1531 time to fit residues: 13.6402 Evaluate side-chains 56 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7718 Z= 0.364 Angle : 0.518 5.693 10478 Z= 0.286 Chirality : 0.044 0.138 1158 Planarity : 0.003 0.046 1336 Dihedral : 4.153 17.451 994 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.71 % Allowed : 9.17 % 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: 0.86 (0.28), residues: 906 helix: 1.34 (0.31), residues: 302 sheet: -0.18 (0.48), residues: 130 loop : 0.44 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 344 HIS 0.009 0.001 HIS A 0 PHE 0.023 0.001 PHE B 506 TYR 0.018 0.002 TYR B 471 ARG 0.005 0.000 ARG B 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 58 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.9010 (m-30) cc_final: 0.8617 (t0) REVERT: A 249 LYS cc_start: 0.8935 (tmtt) cc_final: 0.8713 (ttmm) REVERT: A 272 ASN cc_start: 0.9329 (t0) cc_final: 0.9016 (p0) REVERT: A 311 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 326 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8732 (t) REVERT: A 473 MET cc_start: 0.9046 (mmm) cc_final: 0.8718 (mmm) REVERT: B 57 GLU cc_start: 0.8814 (mp0) cc_final: 0.8463 (mp0) REVERT: B 58 LEU cc_start: 0.9173 (mm) cc_final: 0.8701 (pp) REVERT: B 173 ASP cc_start: 0.9010 (m-30) cc_final: 0.8579 (t0) REVERT: B 272 ASN cc_start: 0.9300 (OUTLIER) cc_final: 0.9001 (m-40) REVERT: B 274 ASN cc_start: 0.8561 (m-40) cc_final: 0.7950 (p0) REVERT: B 389 MET cc_start: 0.8625 (tpp) cc_final: 0.8221 (ttt) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.1736 time to fit residues: 14.7680 Evaluate side-chains 56 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 272 ASN Chi-restraints excluded: chain B residue 436 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3363 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= 0.170 Angle : 0.446 5.961 10478 Z= 0.245 Chirality : 0.042 0.146 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.931 16.777 994 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.71 % Allowed : 9.29 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.28), residues: 906 helix: 1.45 (0.30), residues: 302 sheet: -0.05 (0.49), residues: 130 loop : 0.43 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.008 0.001 HIS A 0 PHE 0.014 0.001 PHE A 506 TYR 0.012 0.001 TYR B 471 ARG 0.002 0.000 ARG A 95 *********************** 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 62 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8980 (m-30) cc_final: 0.8580 (t0) REVERT: A 249 LYS cc_start: 0.8899 (tmtt) cc_final: 0.8681 (ttmm) REVERT: A 272 ASN cc_start: 0.9283 (t0) cc_final: 0.8959 (p0) REVERT: A 311 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 326 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8734 (t) REVERT: A 473 MET cc_start: 0.9033 (mmm) cc_final: 0.8709 (mmm) REVERT: B 57 GLU cc_start: 0.8764 (mp0) cc_final: 0.8437 (mp0) REVERT: B 58 LEU cc_start: 0.9201 (mm) cc_final: 0.8745 (pp) REVERT: B 173 ASP cc_start: 0.8996 (m-30) cc_final: 0.8535 (t0) REVERT: B 272 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8990 (m-40) REVERT: B 274 ASN cc_start: 0.8501 (m-40) cc_final: 0.7957 (p0) REVERT: B 473 MET cc_start: 0.8964 (mmm) cc_final: 0.8746 (mmm) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.1666 time to fit residues: 15.0552 Evaluate side-chains 57 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7718 Z= 0.162 Angle : 0.441 6.506 10478 Z= 0.242 Chirality : 0.042 0.144 1158 Planarity : 0.003 0.044 1336 Dihedral : 3.823 16.074 994 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.60 % Allowed : 9.76 % Favored : 89.64 % 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: 0.99 (0.28), residues: 906 helix: 1.55 (0.30), residues: 302 sheet: -0.02 (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 0.001 0.000 HIS B 456 PHE 0.014 0.001 PHE B 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 61 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8979 (m-30) cc_final: 0.8577 (t0) REVERT: A 249 LYS cc_start: 0.8904 (tmtt) cc_final: 0.8679 (ttmm) REVERT: A 272 ASN cc_start: 0.9277 (t0) cc_final: 0.8948 (p0) REVERT: A 311 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 326 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8724 (t) REVERT: A 365 CYS cc_start: 0.7847 (t) cc_final: 0.7591 (p) REVERT: A 473 MET cc_start: 0.9062 (mmm) cc_final: 0.8726 (mmm) REVERT: A 506 PHE cc_start: 0.8770 (t80) cc_final: 0.8342 (m-80) REVERT: B 57 GLU cc_start: 0.8755 (mp0) cc_final: 0.8487 (mp0) REVERT: B 58 LEU cc_start: 0.9207 (mm) cc_final: 0.8735 (pp) REVERT: B 173 ASP cc_start: 0.8987 (m-30) cc_final: 0.8523 (t0) REVERT: B 272 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.9033 (m-40) REVERT: B 274 ASN cc_start: 0.8525 (m-40) cc_final: 0.8022 (p0) REVERT: B 473 MET cc_start: 0.8985 (mmm) cc_final: 0.8772 (mmm) outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.1449 time to fit residues: 13.1642 Evaluate side-chains 57 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 67 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3275 r_free = 0.3275 target = 0.074946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060705 restraints weight = 18976.215| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.27 r_work: 0.2825 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3448 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= 0.177 Angle : 0.444 6.257 10478 Z= 0.243 Chirality : 0.042 0.143 1158 Planarity : 0.003 0.044 1336 Dihedral : 3.792 16.253 994 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 10.00 % Favored : 89.29 % 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: 1.00 (0.28), residues: 906 helix: 1.55 (0.30), residues: 302 sheet: 0.00 (0.48), residues: 130 loop : 0.41 (0.29), residues: 474 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 0.013 0.001 PHE B 506 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: 1583.70 seconds wall clock time: 29 minutes 10.53 seconds (1750.53 seconds total)