Starting phenix.real_space_refine on Tue May 7 09:17:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/05_2024/8ur6_42484.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/05_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_42484/05_2024/8ur6_42484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/05_2024/8ur6_42484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/05_2024/8ur6_42484.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur6_42484/05_2024/8ur6_42484.pdb" } 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-5322/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: 4.46, 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: 2.96 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: 0.92 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: 2.45 Time building geometry restraints manager: 3.21 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 2.440 nonbonded pdb=" OG SER B 431 " pdb=" OD1 ASN B 433 " model vdw 2.236 2.440 nonbonded pdb=" OG SER A 347 " pdb=" NE1 TRP A 410 " model vdw 2.293 2.520 nonbonded pdb=" OG SER B 347 " pdb=" NE1 TRP B 410 " model vdw 2.294 2.520 nonbonded pdb=" O THR B 185 " pdb=" OH TYR B 412 " model vdw 2.297 2.440 ... (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 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: 0.710 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: 4.000 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.670 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- 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 : 0.880 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: 0.1960 time to fit residues: 35.0633 Evaluate side-chains 75 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 2.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8436 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7718 Z= 0.283 Angle : 0.484 5.630 10478 Z= 0.266 Chirality : 0.044 0.150 1158 Planarity : 0.004 0.061 1336 Dihedral : 4.086 18.029 994 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.19 % Allowed : 5.24 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 906 helix: 1.35 (0.31), residues: 300 sheet: -0.01 (0.47), 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 0.025 0.001 PHE A 506 TYR 0.017 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 86 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8980 (m-30) cc_final: 0.8617 (t0) REVERT: A 249 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8519 (ttmm) REVERT: A 311 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 465 MET cc_start: 0.9324 (mtm) cc_final: 0.9043 (mtt) REVERT: A 473 MET cc_start: 0.9077 (mmm) cc_final: 0.8736 (mmm) REVERT: B 58 LEU cc_start: 0.8997 (mm) cc_final: 0.8609 (pp) REVERT: B 159 GLU cc_start: 0.8862 (mp0) cc_final: 0.8491 (tp30) REVERT: B 173 ASP cc_start: 0.8991 (m-30) cc_final: 0.8540 (t0) outliers start: 10 outliers final: 5 residues processed: 78 average time/residue: 0.1727 time to fit residues: 19.7847 Evaluate side-chains 67 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 103 ASP 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: 3.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7718 Z= 0.183 Angle : 0.432 4.756 10478 Z= 0.236 Chirality : 0.042 0.149 1158 Planarity : 0.003 0.047 1336 Dihedral : 3.833 18.003 994 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.31 % Allowed : 6.43 % 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: 0.75 (0.28), residues: 906 helix: 1.52 (0.30), residues: 302 sheet: 0.02 (0.47), residues: 130 loop : 0.05 (0.27), 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 0.013 0.001 TYR B 236 ARG 0.003 0.000 ARG A 324 *********************** 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 79 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8977 (m-30) cc_final: 0.8591 (t0) REVERT: A 311 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 465 MET cc_start: 0.9311 (mtm) cc_final: 0.9016 (mtt) REVERT: A 473 MET cc_start: 0.9058 (mmm) cc_final: 0.8722 (mmm) REVERT: B 157 ASN cc_start: 0.7961 (t0) cc_final: 0.6702 (t0) REVERT: B 173 ASP cc_start: 0.8973 (m-30) cc_final: 0.8514 (t0) REVERT: B 272 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8893 (p0) outliers start: 11 outliers final: 3 residues processed: 72 average time/residue: 0.1645 time to fit residues: 17.4382 Evaluate side-chains 61 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 103 ASP 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 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8439 moved from start: 0.2766 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= 0.215 Angle : 0.440 4.710 10478 Z= 0.242 Chirality : 0.042 0.147 1158 Planarity : 0.003 0.045 1336 Dihedral : 3.870 18.154 994 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.83 % Allowed : 7.74 % Favored : 91.43 % 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: 1.63 (0.31), residues: 302 sheet: 0.10 (0.48), residues: 130 loop : 0.21 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.005 0.001 HIS B 207 PHE 0.017 0.001 PHE A 506 TYR 0.014 0.001 TYR B 412 ARG 0.003 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 66 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8978 (m-30) cc_final: 0.8585 (t0) REVERT: A 311 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 465 MET cc_start: 0.9319 (mtm) cc_final: 0.8967 (mtp) REVERT: A 473 MET cc_start: 0.9077 (mmm) cc_final: 0.8758 (mmm) REVERT: B 173 ASP cc_start: 0.9021 (m-30) cc_final: 0.8556 (t0) REVERT: B 448 ASP cc_start: 0.8874 (m-30) cc_final: 0.8666 (p0) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.1728 time to fit residues: 15.6032 Evaluate side-chains 60 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP 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: 0.8980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7718 Z= 0.283 Angle : 0.465 4.769 10478 Z= 0.256 Chirality : 0.043 0.145 1158 Planarity : 0.003 0.045 1336 Dihedral : 3.982 18.502 994 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.07 % Allowed : 8.21 % Favored : 90.71 % 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: 0.92 (0.28), residues: 906 helix: 1.48 (0.31), residues: 302 sheet: 0.13 (0.49), residues: 130 loop : 0.30 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.006 0.001 HIS A 207 PHE 0.019 0.001 PHE B 506 TYR 0.016 0.001 TYR B 236 ARG 0.004 0.000 ARG A 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 65 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8998 (m-30) cc_final: 0.8598 (t0) REVERT: A 311 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 465 MET cc_start: 0.9317 (mtm) cc_final: 0.9114 (mtp) REVERT: A 473 MET cc_start: 0.9066 (mmm) cc_final: 0.8744 (mmm) REVERT: B 173 ASP cc_start: 0.9048 (m-30) cc_final: 0.8603 (t0) REVERT: B 272 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.9012 (p0) REVERT: B 526 ASP cc_start: 0.8452 (t0) cc_final: 0.8120 (t0) outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.1721 time to fit residues: 15.9944 Evaluate side-chains 55 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 156 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: 3.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.0070 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3144 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= 0.207 Angle : 0.437 4.760 10478 Z= 0.241 Chirality : 0.042 0.146 1158 Planarity : 0.003 0.042 1336 Dihedral : 3.873 17.738 994 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.83 % Allowed : 9.17 % 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: 0.96 (0.28), residues: 906 helix: 1.54 (0.31), residues: 302 sheet: 0.08 (0.48), residues: 130 loop : 0.33 (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 0.014 0.001 PHE A 506 TYR 0.015 0.001 TYR B 412 ARG 0.003 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 59 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8991 (m-30) cc_final: 0.8583 (t0) REVERT: A 311 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 473 MET cc_start: 0.9070 (mmm) cc_final: 0.8753 (mmm) REVERT: B 173 ASP cc_start: 0.9013 (m-30) cc_final: 0.8567 (t0) REVERT: B 526 ASP cc_start: 0.8476 (t0) cc_final: 0.8124 (t0) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 0.1497 time to fit residues: 12.7783 Evaluate side-chains 52 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 103 ASP 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: 0.0770 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.0770 chunk 52 optimal weight: 4.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7718 Z= 0.175 Angle : 0.422 4.699 10478 Z= 0.234 Chirality : 0.042 0.144 1158 Planarity : 0.003 0.041 1336 Dihedral : 3.790 17.008 994 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.48 % Allowed : 10.00 % Favored : 89.52 % 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: 1.60 (0.31), residues: 302 sheet: 0.20 (0.48), residues: 130 loop : 0.31 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 192 HIS 0.004 0.001 HIS B 0 PHE 0.013 0.001 PHE B 506 TYR 0.014 0.001 TYR A 412 ARG 0.002 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 59 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8988 (m-30) cc_final: 0.8584 (t0) REVERT: A 311 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 473 MET cc_start: 0.9071 (mmm) cc_final: 0.8760 (mmm) REVERT: B 173 ASP cc_start: 0.9000 (m-30) cc_final: 0.8559 (t0) REVERT: B 526 ASP cc_start: 0.8492 (t0) cc_final: 0.8164 (t0) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 0.1384 time to fit residues: 12.3066 Evaluate side-chains 55 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 103 ASP 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: 0.9980 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3228 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= 0.182 Angle : 0.418 4.712 10478 Z= 0.230 Chirality : 0.042 0.145 1158 Planarity : 0.003 0.044 1336 Dihedral : 3.736 16.774 994 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.60 % Allowed : 10.36 % Favored : 89.05 % 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: 1.61 (0.31), residues: 302 sheet: 0.29 (0.48), 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 0.002 0.000 HIS B 456 PHE 0.015 0.001 PHE A 506 TYR 0.016 0.001 TYR A 412 ARG 0.002 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: 5 poor density : 53 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8987 (m-30) cc_final: 0.8581 (t0) REVERT: A 311 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 473 MET cc_start: 0.9071 (mmm) cc_final: 0.8752 (mmm) REVERT: B 173 ASP cc_start: 0.8996 (m-30) cc_final: 0.8552 (t0) REVERT: B 526 ASP cc_start: 0.8495 (t0) cc_final: 0.8157 (t0) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1454 time to fit residues: 12.3680 Evaluate side-chains 54 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 103 ASP 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: 0.9980 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7718 Z= 0.176 Angle : 0.420 4.710 10478 Z= 0.230 Chirality : 0.042 0.144 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.735 17.061 994 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.60 % Allowed : 10.60 % 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: 1.09 (0.28), residues: 906 helix: 1.61 (0.31), residues: 302 sheet: 0.32 (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 0.004 0.001 HIS B 0 PHE 0.015 0.001 PHE A 506 TYR 0.016 0.001 TYR B 412 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 56 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8987 (m-30) cc_final: 0.8582 (t0) REVERT: A 311 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 473 MET cc_start: 0.9065 (mmm) cc_final: 0.8746 (mmm) REVERT: B 173 ASP cc_start: 0.8993 (m-30) cc_final: 0.8548 (t0) REVERT: B 526 ASP cc_start: 0.8501 (t0) cc_final: 0.8163 (t0) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1509 time to fit residues: 12.4744 Evaluate side-chains 54 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain B residue 103 ASP 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: 0.5980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7718 Z= 0.149 Angle : 0.407 4.704 10478 Z= 0.223 Chirality : 0.041 0.145 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.660 18.085 994 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.48 % Allowed : 10.95 % 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: 1.16 (0.28), residues: 906 helix: 1.69 (0.31), residues: 302 sheet: 0.38 (0.49), 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 0.002 0.000 HIS B 0 PHE 0.013 0.001 PHE A 506 TYR 0.015 0.001 TYR B 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 60 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8487 (mmtm) REVERT: A 173 ASP cc_start: 0.8979 (m-30) cc_final: 0.8573 (t0) REVERT: A 311 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7935 (tm-30) REVERT: A 473 MET cc_start: 0.9050 (mmm) cc_final: 0.8731 (mmm) REVERT: B 173 ASP cc_start: 0.9005 (m-30) cc_final: 0.8562 (t0) REVERT: B 526 ASP cc_start: 0.8477 (t0) cc_final: 0.8161 (t0) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1494 time to fit residues: 13.1848 Evaluate side-chains 53 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 436 CYS 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 489 GLN 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 = 0.076392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062093 restraints weight = 18754.017| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.23 r_work: 0.2824 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7718 Z= 0.167 Angle : 0.414 4.704 10478 Z= 0.226 Chirality : 0.042 0.144 1158 Planarity : 0.003 0.043 1336 Dihedral : 3.682 18.523 994 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.60 % Allowed : 11.55 % Favored : 87.86 % 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: 1.17 (0.28), residues: 906 helix: 1.67 (0.31), residues: 302 sheet: 0.44 (0.49), 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 0.002 0.000 HIS B 456 PHE 0.010 0.001 PHE B 506 TYR 0.015 0.001 TYR B 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: 1625.98 seconds wall clock time: 30 minutes 31.17 seconds (1831.17 seconds total)