Starting phenix.real_space_refine on Wed Feb 14 01:25:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh7_27431/02_2024/8dh7_27431.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh7_27431/02_2024/8dh7_27431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh7_27431/02_2024/8dh7_27431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh7_27431/02_2024/8dh7_27431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh7_27431/02_2024/8dh7_27431.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dh7_27431/02_2024/8dh7_27431.pdb" } resolution = 2.99 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= 0.079 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 34 5.16 5 C 5240 2.51 5 N 1454 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 178": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8274 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4137 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Chain: "A" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4137 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 491} Time building chain proxies: 4.91, per 1000 atoms: 0.59 Number of scatterers: 8274 At special positions: 0 Unit cell: (113.016, 82.269, 78.945, 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 34 16.00 O 1546 8.00 N 1454 7.00 C 5240 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 39.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.964A pdb=" N VAL B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 30 removed outlier: 3.594A pdb=" N ILE B 27 " --> pdb=" O HIS B 24 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 78 through 87 removed outlier: 3.831A pdb=" N ASN B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 246 through 264 Processing helix chain 'B' and resid 279 through 291 Processing helix chain 'B' and resid 305 through 315 removed outlier: 4.024A pdb=" N LEU B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.567A pdb=" N HIS B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 396 through 404 removed outlier: 3.534A pdb=" N ARG B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 471 through 493 removed outlier: 4.566A pdb=" N ALA B 476 " --> pdb=" O PRO B 472 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 515 Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.929A pdb=" N VAL A 20 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 30 removed outlier: 3.710A pdb=" N ILE A 27 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.921A pdb=" N ASN A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 246 through 264 Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.772A pdb=" N ASP A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.760A pdb=" N ASN A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 396 through 404 removed outlier: 3.686A pdb=" N ASN A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 471 through 493 removed outlier: 4.558A pdb=" N ALA A 476 " --> pdb=" O PRO A 472 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 515 Processing sheet with id=AA1, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.420A pdb=" N ILE B 91 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE B 69 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG B 93 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 71 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 36 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 35 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE B 144 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 37 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLU B 146 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 141 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 174 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N ASP B 173 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N ALA B 227 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL B 175 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL B 229 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 177 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER B 231 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL B 179 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.713A pdb=" N ALA B 149 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 191 removed outlier: 8.429A pdb=" N CYS B 347 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 320 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ARG B 349 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA B 322 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 297 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 320 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.865A pdb=" N MET B 368 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER B 407 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL B 445 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET B 409 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AA6, first strand: chain 'B' and resid 380 through 381 removed outlier: 6.734A pdb=" N VAL B 374 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AA8, first strand: chain 'B' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.427A pdb=" N ILE A 91 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE A 69 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG A 93 " --> pdb=" O PHE A 69 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 71 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 36 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR A 35 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 144 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY A 37 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLU A 146 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP A 141 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N ASP A 173 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ALA A 227 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 175 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL A 229 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 177 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER A 231 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 179 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.653A pdb=" N ALA A 149 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191 removed outlier: 8.411A pdb=" N CYS A 347 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA A 320 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG A 349 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA A 322 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 297 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA A 320 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 274 through 275 removed outlier: 5.943A pdb=" N ALA A 367 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HIS A 410 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN A 369 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER A 407 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 445 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET A 409 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AB5, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.617A pdb=" N VAL A 374 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AB7, first strand: chain 'A' and resid 414 through 415 283 hydrogen bonds defined for protein. 795 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: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1668 1.33 - 1.45: 1918 1.45 - 1.57: 4823 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 8470 Sorted by residual: bond pdb=" CA ASP B 245 " pdb=" C ASP B 245 " ideal model delta sigma weight residual 1.523 1.455 0.069 1.80e-02 3.09e+03 1.45e+01 bond pdb=" CA ASP A 245 " pdb=" C ASP A 245 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.80e-02 3.09e+03 1.39e+01 bond pdb=" CA GLN B 275 " pdb=" CB GLN B 275 " ideal model delta sigma weight residual 1.527 1.606 -0.078 2.48e-02 1.63e+03 9.99e+00 bond pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta sigma weight residual 1.457 1.415 0.042 1.40e-02 5.10e+03 9.02e+00 bond pdb=" N ASP A 245 " pdb=" CA ASP A 245 " ideal model delta sigma weight residual 1.457 1.416 0.041 1.40e-02 5.10e+03 8.45e+00 ... (remaining 8465 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.17: 233 105.17 - 112.40: 4290 112.40 - 119.64: 2934 119.64 - 126.87: 3905 126.87 - 134.10: 132 Bond angle restraints: 11494 Sorted by residual: angle pdb=" N MET B 246 " pdb=" CA MET B 246 " pdb=" C MET B 246 " ideal model delta sigma weight residual 113.41 101.89 11.52 1.22e+00 6.72e-01 8.92e+01 angle pdb=" N MET A 246 " pdb=" CA MET A 246 " pdb=" C MET A 246 " ideal model delta sigma weight residual 113.12 102.23 10.89 1.25e+00 6.40e-01 7.60e+01 angle pdb=" CA GLN B 275 " pdb=" CB GLN B 275 " pdb=" CG GLN B 275 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA ASP B 244 " pdb=" C ASP B 244 " pdb=" O ASP B 244 " ideal model delta sigma weight residual 121.78 117.29 4.49 1.28e+00 6.10e-01 1.23e+01 angle pdb=" CA ASP A 244 " pdb=" C ASP A 244 " pdb=" O ASP A 244 " ideal model delta sigma weight residual 121.78 117.38 4.40 1.28e+00 6.10e-01 1.18e+01 ... (remaining 11489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4711 17.05 - 34.10: 344 34.10 - 51.15: 62 51.15 - 68.19: 16 68.19 - 85.24: 7 Dihedral angle restraints: 5140 sinusoidal: 2096 harmonic: 3044 Sorted by residual: dihedral pdb=" CA ASP B 452 " pdb=" CB ASP B 452 " pdb=" CG ASP B 452 " pdb=" OD1 ASP B 452 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP A 447 " pdb=" CB ASP A 447 " pdb=" CG ASP A 447 " pdb=" OD1 ASP A 447 " ideal model delta sinusoidal sigma weight residual -30.00 -86.79 56.79 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP B 447 " pdb=" CB ASP B 447 " pdb=" CG ASP B 447 " pdb=" OD1 ASP B 447 " ideal model delta sinusoidal sigma weight residual -30.00 -86.16 56.16 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 5137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1008 0.053 - 0.107: 212 0.107 - 0.160: 44 0.160 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 1268 Sorted by residual: chirality pdb=" CA MET B 246 " pdb=" N MET B 246 " pdb=" C MET B 246 " pdb=" CB MET B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET A 246 " pdb=" N MET A 246 " pdb=" C MET A 246 " pdb=" CB MET A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP A 245 " pdb=" N ASP A 245 " pdb=" C ASP A 245 " pdb=" CB ASP A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1265 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 244 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C ASP A 244 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 244 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 245 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 244 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ASP B 244 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP B 244 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 245 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 94 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO B 95 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.027 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 162 2.67 - 3.23: 7752 3.23 - 3.79: 13074 3.79 - 4.34: 19126 4.34 - 4.90: 31483 Nonbonded interactions: 71597 Sorted by model distance: nonbonded pdb=" O LEU B 317 " pdb=" NH2 ARG B 345 " model vdw 2.117 2.520 nonbonded pdb=" O ASP A 211 " pdb=" NH2 ARG A 349 " model vdw 2.134 2.520 nonbonded pdb=" NZ LYS B 506 " pdb=" O SER B 521 " model vdw 2.178 2.520 nonbonded pdb=" O ASP B 211 " pdb=" NH2 ARG B 349 " model vdw 2.179 2.520 nonbonded pdb=" O PHE B 168 " pdb=" OG SER B 172 " model vdw 2.198 2.440 ... (remaining 71592 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: 4.730 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: 13.670 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.730 Find NCS groups from input model: 0.410 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.003 0.078 8470 Z= 0.234 Angle : 0.594 11.524 11494 Z= 0.339 Chirality : 0.047 0.266 1268 Planarity : 0.005 0.053 1514 Dihedral : 12.958 85.242 3172 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.55 % Allowed : 0.11 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.73 (0.27), residues: 1048 helix: 1.12 (0.28), residues: 384 sheet: 1.15 (0.50), residues: 96 loop : 0.01 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 84 HIS 0.004 0.001 HIS A 492 PHE 0.018 0.001 PHE B 507 TYR 0.006 0.001 TYR B 13 ARG 0.003 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.989 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 121 average time/residue: 1.3178 time to fit residues: 169.2881 Evaluate side-chains 84 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS A 492 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8470 Z= 0.340 Angle : 0.580 5.644 11494 Z= 0.303 Chirality : 0.048 0.141 1268 Planarity : 0.005 0.049 1514 Dihedral : 5.656 52.475 1140 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 1.88 % Allowed : 8.30 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.71 (0.26), residues: 1048 helix: 1.22 (0.27), residues: 364 sheet: 0.69 (0.45), residues: 134 loop : -0.01 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 84 HIS 0.007 0.001 HIS B 410 PHE 0.015 0.002 PHE B 507 TYR 0.008 0.001 TYR B 377 ARG 0.007 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7969 (p0) cc_final: 0.7749 (p0) REVERT: B 246 MET cc_start: 0.7542 (ttm) cc_final: 0.7296 (ttt) REVERT: A 115 ASP cc_start: 0.8020 (p0) cc_final: 0.7814 (p0) REVERT: A 246 MET cc_start: 0.7507 (ttm) cc_final: 0.7252 (ttt) outliers start: 17 outliers final: 6 residues processed: 92 average time/residue: 1.0658 time to fit residues: 105.7360 Evaluate side-chains 80 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 244 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8470 Z= 0.294 Angle : 0.547 5.849 11494 Z= 0.285 Chirality : 0.047 0.140 1268 Planarity : 0.005 0.049 1514 Dihedral : 5.401 54.803 1134 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 1.66 % Allowed : 10.07 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.61 (0.26), residues: 1048 helix: 1.11 (0.26), residues: 376 sheet: 0.60 (0.46), residues: 134 loop : -0.07 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS B 410 PHE 0.011 0.001 PHE A 336 TYR 0.007 0.001 TYR B 127 ARG 0.006 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: B 246 MET cc_start: 0.7518 (ttm) cc_final: 0.7279 (ttt) REVERT: B 304 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 246 MET cc_start: 0.7528 (ttm) cc_final: 0.7286 (ttt) REVERT: A 304 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7996 (mp) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 1.0588 time to fit residues: 99.7937 Evaluate side-chains 86 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 0.0570 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 GLN B 344 HIS B 369 ASN A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8470 Z= 0.173 Angle : 0.493 5.589 11494 Z= 0.256 Chirality : 0.044 0.137 1268 Planarity : 0.005 0.050 1514 Dihedral : 5.205 57.518 1134 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 1.77 % Allowed : 11.28 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.77 (0.26), residues: 1048 helix: 1.34 (0.27), residues: 378 sheet: 0.56 (0.46), residues: 134 loop : -0.02 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 499 PHE 0.010 0.001 PHE A 336 TYR 0.006 0.001 TYR B 127 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 304 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7979 (mp) REVERT: B 327 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6927 (pp) REVERT: A 246 MET cc_start: 0.7443 (ttm) cc_final: 0.7158 (ttt) REVERT: A 304 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7938 (mp) outliers start: 16 outliers final: 3 residues processed: 92 average time/residue: 1.0093 time to fit residues: 100.6760 Evaluate side-chains 80 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS B 492 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8470 Z= 0.239 Angle : 0.521 6.530 11494 Z= 0.268 Chirality : 0.045 0.158 1268 Planarity : 0.005 0.050 1514 Dihedral : 5.283 57.969 1134 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 1.66 % Allowed : 12.61 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.26), residues: 1048 helix: 1.24 (0.27), residues: 390 sheet: 0.49 (0.46), residues: 134 loop : -0.08 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.006 0.001 HIS B 492 PHE 0.010 0.001 PHE A 336 TYR 0.007 0.001 TYR B 142 ARG 0.004 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: B 304 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 156 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 246 MET cc_start: 0.7427 (ttm) cc_final: 0.7200 (ttt) REVERT: A 304 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7973 (mp) outliers start: 15 outliers final: 8 residues processed: 92 average time/residue: 0.9223 time to fit residues: 92.8170 Evaluate side-chains 89 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN B 344 HIS B 356 ASN B 369 ASN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 492 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8470 Z= 0.358 Angle : 0.578 5.513 11494 Z= 0.298 Chirality : 0.048 0.153 1268 Planarity : 0.005 0.048 1514 Dihedral : 5.511 56.084 1134 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 2.77 % Allowed : 13.16 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.26), residues: 1048 helix: 1.07 (0.27), residues: 390 sheet: 0.38 (0.46), residues: 134 loop : -0.18 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.006 0.001 HIS B 96 PHE 0.011 0.002 PHE A 336 TYR 0.007 0.001 TYR B 142 ARG 0.004 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.984 Fit side-chains REVERT: B 304 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8103 (mp) REVERT: B 327 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7208 (pp) REVERT: A 115 ASP cc_start: 0.8065 (p0) cc_final: 0.7860 (p0) REVERT: A 156 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8515 (mt) REVERT: A 304 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8074 (mp) outliers start: 25 outliers final: 12 residues processed: 93 average time/residue: 1.0185 time to fit residues: 102.7530 Evaluate side-chains 92 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 59 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 197 ASN B 275 GLN B 344 HIS B 369 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN A 436 GLN A 492 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8470 Z= 0.236 Angle : 0.526 5.519 11494 Z= 0.271 Chirality : 0.045 0.149 1268 Planarity : 0.005 0.049 1514 Dihedral : 5.367 56.475 1134 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 2.77 % Allowed : 13.72 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.66 (0.26), residues: 1048 helix: 1.36 (0.27), residues: 378 sheet: 0.35 (0.46), residues: 134 loop : -0.13 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 96 PHE 0.011 0.001 PHE A 336 TYR 0.007 0.001 TYR B 142 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.175 Fit side-chains REVERT: B 115 ASP cc_start: 0.8000 (p0) cc_final: 0.7750 (p0) REVERT: B 304 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 327 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7164 (pp) REVERT: B 523 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6796 (mt-10) REVERT: A 156 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 304 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8007 (mp) outliers start: 25 outliers final: 11 residues processed: 102 average time/residue: 1.0249 time to fit residues: 113.1388 Evaluate side-chains 93 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS B 369 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS A 493 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8470 Z= 0.223 Angle : 0.530 6.307 11494 Z= 0.271 Chirality : 0.045 0.145 1268 Planarity : 0.005 0.049 1514 Dihedral : 5.314 56.517 1134 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 2.54 % Allowed : 14.60 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.64 (0.27), residues: 1048 helix: 1.30 (0.27), residues: 390 sheet: 0.31 (0.46), residues: 134 loop : -0.13 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS B 96 PHE 0.017 0.001 PHE B 312 TYR 0.007 0.001 TYR B 142 ARG 0.007 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.944 Fit side-chains REVERT: B 304 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 327 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7246 (pp) REVERT: B 523 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6753 (mt-10) REVERT: A 156 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 304 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8023 (mp) outliers start: 23 outliers final: 12 residues processed: 95 average time/residue: 0.9613 time to fit residues: 99.3968 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 GLN B 344 HIS B 369 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8470 Z= 0.165 Angle : 0.505 5.520 11494 Z= 0.259 Chirality : 0.044 0.144 1268 Planarity : 0.005 0.050 1514 Dihedral : 5.204 57.250 1134 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.42 % Rotamer: Outliers : 2.21 % Allowed : 14.93 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.77 (0.27), residues: 1048 helix: 1.44 (0.27), residues: 390 sheet: 0.31 (0.46), residues: 134 loop : -0.06 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 339 HIS 0.004 0.001 HIS B 499 PHE 0.017 0.001 PHE B 312 TYR 0.006 0.001 TYR B 142 ARG 0.007 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.035 Fit side-chains REVERT: B 115 ASP cc_start: 0.7964 (p0) cc_final: 0.7709 (p0) REVERT: B 304 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8108 (mp) REVERT: B 327 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7204 (pp) REVERT: B 523 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 156 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8478 (mt) REVERT: A 304 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 327 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7096 (pp) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.9285 time to fit residues: 97.2516 Evaluate side-chains 94 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS B 369 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8470 Z= 0.187 Angle : 0.512 6.015 11494 Z= 0.262 Chirality : 0.045 0.143 1268 Planarity : 0.005 0.050 1514 Dihedral : 5.232 57.135 1134 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.33 % Rotamer: Outliers : 2.54 % Allowed : 15.04 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.27), residues: 1048 helix: 1.49 (0.27), residues: 390 sheet: 0.34 (0.46), residues: 134 loop : -0.08 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 339 HIS 0.004 0.001 HIS A 492 PHE 0.016 0.001 PHE B 312 TYR 0.006 0.001 TYR B 142 ARG 0.006 0.000 ARG A 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 1.002 Fit side-chains REVERT: B 115 ASP cc_start: 0.7967 (p0) cc_final: 0.7744 (p0) REVERT: B 246 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7314 (mtm) REVERT: B 304 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 327 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7258 (pp) REVERT: B 523 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 156 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8498 (mt) REVERT: A 304 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 327 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7091 (pp) outliers start: 23 outliers final: 11 residues processed: 94 average time/residue: 0.9565 time to fit residues: 97.8020 Evaluate side-chains 92 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 275 GLN B 344 HIS B 369 ASN ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113476 restraints weight = 9746.444| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.62 r_work: 0.3199 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8470 Z= 0.203 Angle : 0.515 5.774 11494 Z= 0.264 Chirality : 0.045 0.144 1268 Planarity : 0.005 0.050 1514 Dihedral : 5.271 56.431 1134 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 2.10 % Allowed : 15.82 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.79 (0.27), residues: 1048 helix: 1.51 (0.27), residues: 390 sheet: 0.36 (0.46), residues: 134 loop : -0.12 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 339 HIS 0.006 0.001 HIS A 492 PHE 0.016 0.001 PHE B 312 TYR 0.007 0.001 TYR B 142 ARG 0.006 0.000 ARG A 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.56 seconds wall clock time: 49 minutes 26.51 seconds (2966.51 seconds total)