Starting phenix.real_space_refine on Mon Aug 5 08:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wwp_37895/08_2024/8wwp_37895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wwp_37895/08_2024/8wwp_37895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wwp_37895/08_2024/8wwp_37895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wwp_37895/08_2024/8wwp_37895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wwp_37895/08_2024/8wwp_37895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wwp_37895/08_2024/8wwp_37895.cif" } resolution = 3.12 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= 1.000 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 48 5.16 5 C 8243 2.51 5 N 2271 2.21 5 O 2563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 567": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4375 Classifications: {'peptide': 583} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 552} Chain: "B" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4368 Classifications: {'peptide': 582} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 551} Chain: "C" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4382 Classifications: {'peptide': 584} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 553} Time building chain proxies: 9.75, per 1000 atoms: 0.74 Number of scatterers: 13125 At special positions: 0 Unit cell: (118.8, 118.8, 96.3, 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 48 16.00 O 2563 8.00 N 2271 7.00 C 8243 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: 5.66 Conformation dependent library (CDL) restraints added in 2.7 seconds 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 35.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.700A pdb=" N PHE A 115 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 154 removed outlier: 4.171A pdb=" N GLY A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.920A pdb=" N GLU A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.509A pdb=" N ALA A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 273 through 282 removed outlier: 4.248A pdb=" N SER A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 320 through 344 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.674A pdb=" N THR A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 removed outlier: 3.565A pdb=" N ILE A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.607A pdb=" N GLY A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 558 through 581 removed outlier: 3.540A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.701A pdb=" N PHE B 115 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 removed outlier: 4.171A pdb=" N GLY B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.920A pdb=" N GLU B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 225 through 236 removed outlier: 3.508A pdb=" N ALA B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 273 through 282 removed outlier: 4.248A pdb=" N SER B 280 " --> pdb=" O TYR B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 320 through 344 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.674A pdb=" N THR B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 removed outlier: 3.565A pdb=" N ILE B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.608A pdb=" N GLY B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 558 through 581 removed outlier: 3.540A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.700A pdb=" N PHE C 115 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 removed outlier: 4.171A pdb=" N GLY C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.920A pdb=" N GLU C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.508A pdb=" N ALA C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 273 through 282 removed outlier: 4.247A pdb=" N SER C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 320 through 344 Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.675A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.565A pdb=" N ILE C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.608A pdb=" N GLY C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'C' and resid 558 through 581 removed outlier: 3.540A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 removed outlier: 6.087A pdb=" N MET A 51 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR A 72 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL A 127 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 74 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE A 129 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 76 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER A 131 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.121A pdb=" N PHE A 187 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP A 188 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 207 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A 203 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA A 539 " --> pdb=" O THR A 546 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU A 548 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS A 537 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 550 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP A 535 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 362 removed outlier: 6.416A pdb=" N GLN A 380 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.518A pdb=" N GLN A 394 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 405 " --> pdb=" O GLN A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.088A pdb=" N MET B 51 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 72 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL B 127 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP B 74 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE B 129 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU B 76 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER B 131 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.121A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP B 188 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 207 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET B 203 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 539 " --> pdb=" O THR B 546 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU B 548 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS B 537 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 550 " --> pdb=" O ASP B 535 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP B 535 " --> pdb=" O LEU B 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.417A pdb=" N GLN B 380 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.518A pdb=" N GLN B 394 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 405 " --> pdb=" O GLN B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.087A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR C 72 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C 127 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP C 74 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE C 129 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU C 76 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER C 131 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175 removed outlier: 4.121A pdb=" N PHE C 187 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP C 188 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C 207 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET C 203 " --> pdb=" O THR C 552 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA C 539 " --> pdb=" O THR C 546 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU C 548 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS C 537 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU C 550 " --> pdb=" O ASP C 535 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP C 535 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 358 through 362 removed outlier: 6.417A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 395 removed outlier: 3.517A pdb=" N GLN C 394 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 405 " --> pdb=" O GLN C 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 651 hydrogen bonds defined for protein. 1809 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: 4.13 Time building geometry restraints manager: 6.15 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: 4521 1.34 - 1.46: 1770 1.46 - 1.57: 6957 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 13335 Sorted by residual: bond pdb=" C ARG C 109 " pdb=" N PRO C 110 " ideal model delta sigma weight residual 1.331 1.343 -0.012 7.90e-03 1.60e+04 2.20e+00 bond pdb=" C ARG A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.331 1.342 -0.011 7.90e-03 1.60e+04 1.84e+00 bond pdb=" C ARG B 109 " pdb=" N PRO B 110 " ideal model delta sigma weight residual 1.331 1.342 -0.010 7.90e-03 1.60e+04 1.64e+00 bond pdb=" CB GLU B 226 " pdb=" CG GLU B 226 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" C ARG B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.339 1.376 -0.037 3.40e-02 8.65e+02 1.17e+00 ... (remaining 13330 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 381 106.71 - 113.54: 7398 113.54 - 120.37: 4879 120.37 - 127.20: 5354 127.20 - 134.03: 96 Bond angle restraints: 18108 Sorted by residual: angle pdb=" C ASP B 299 " pdb=" N GLN B 300 " pdb=" CA GLN B 300 " ideal model delta sigma weight residual 121.54 126.01 -4.47 1.91e+00 2.74e-01 5.47e+00 angle pdb=" C ASP C 299 " pdb=" N GLN C 300 " pdb=" CA GLN C 300 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.43e+00 angle pdb=" C ASP A 299 " pdb=" N GLN A 300 " pdb=" CA GLN A 300 " ideal model delta sigma weight residual 121.54 125.99 -4.45 1.91e+00 2.74e-01 5.42e+00 angle pdb=" C MET C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta sigma weight residual 122.21 118.76 3.45 1.62e+00 3.81e-01 4.52e+00 angle pdb=" C MET B 51 " pdb=" N LEU B 52 " pdb=" CA LEU B 52 " ideal model delta sigma weight residual 122.21 118.80 3.41 1.62e+00 3.81e-01 4.43e+00 ... (remaining 18103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6894 17.70 - 35.39: 923 35.39 - 53.09: 211 53.09 - 70.79: 48 70.79 - 88.48: 21 Dihedral angle restraints: 8097 sinusoidal: 3132 harmonic: 4965 Sorted by residual: dihedral pdb=" CA ASP A 299 " pdb=" C ASP A 299 " pdb=" N GLN A 300 " pdb=" CA GLN A 300 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP C 299 " pdb=" C ASP C 299 " pdb=" N GLN C 300 " pdb=" CA GLN C 300 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP B 299 " pdb=" C ASP B 299 " pdb=" N GLN B 300 " pdb=" CA GLN B 300 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 8094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1212 0.028 - 0.056: 561 0.056 - 0.084: 186 0.084 - 0.112: 122 0.112 - 0.140: 43 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA ILE C 17 " pdb=" N ILE C 17 " pdb=" C ILE C 17 " pdb=" CB ILE C 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 17 " pdb=" N ILE B 17 " pdb=" C ILE B 17 " pdb=" CB ILE B 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 17 " pdb=" N ILE A 17 " pdb=" C ILE A 17 " pdb=" CB ILE A 17 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2121 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 16 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C THR C 16 " 0.030 2.00e-02 2.50e+03 pdb=" O THR C 16 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 17 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 16 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C THR A 16 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 16 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 17 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 16 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C THR B 16 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 16 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE B 17 " 0.010 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3059 2.79 - 3.32: 11935 3.32 - 3.84: 20710 3.84 - 4.37: 22298 4.37 - 4.90: 40790 Nonbonded interactions: 98792 Sorted by model distance: nonbonded pdb=" N GLU B 226 " pdb=" OE1 GLU B 226 " model vdw 2.262 3.120 nonbonded pdb=" N GLU A 226 " pdb=" OE1 GLU A 226 " model vdw 2.263 3.120 nonbonded pdb=" N GLU C 226 " pdb=" OE1 GLU C 226 " model vdw 2.263 3.120 nonbonded pdb=" O TYR A 275 " pdb=" OG SER A 279 " model vdw 2.302 3.040 nonbonded pdb=" O TYR B 275 " pdb=" OG SER B 279 " model vdw 2.302 3.040 ... (remaining 98787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 596) selection = chain 'B' selection = (chain 'C' and resid 15 through 596) } 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: 0.530 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 42.090 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 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 0.037 13335 Z= 0.201 Angle : 0.507 5.959 18108 Z= 0.269 Chirality : 0.043 0.140 2124 Planarity : 0.003 0.023 2400 Dihedral : 17.165 88.484 4911 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 0.07 % Allowed : 30.58 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.23 (0.21), residues: 1743 helix: 1.54 (0.23), residues: 552 sheet: 0.41 (0.24), residues: 426 loop : -1.03 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 173 HIS 0.001 0.000 HIS C 369 PHE 0.011 0.001 PHE B 536 TYR 0.013 0.001 TYR B 45 ARG 0.002 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.466 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.2035 time to fit residues: 41.9559 Evaluate side-chains 125 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13335 Z= 0.231 Angle : 0.536 6.568 18108 Z= 0.278 Chirality : 0.044 0.157 2124 Planarity : 0.003 0.023 2400 Dihedral : 3.874 19.748 1893 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.39 % Allowed : 29.57 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.51 (0.21), residues: 1743 helix: 1.68 (0.23), residues: 554 sheet: 0.70 (0.25), residues: 423 loop : -0.87 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.002 0.001 HIS B 410 PHE 0.013 0.001 PHE B 68 TYR 0.027 0.002 TYR C 45 ARG 0.002 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.385 Fit side-chains REVERT: B 155 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7519 (mt) REVERT: C 155 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7233 (mt) outliers start: 33 outliers final: 18 residues processed: 163 average time/residue: 0.1874 time to fit residues: 49.2625 Evaluate side-chains 153 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 156 optimal weight: 0.0040 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13335 Z= 0.233 Angle : 0.539 6.630 18108 Z= 0.281 Chirality : 0.044 0.147 2124 Planarity : 0.004 0.031 2400 Dihedral : 4.000 18.649 1893 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.65 % Allowed : 28.12 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.52 (0.21), residues: 1743 helix: 1.66 (0.23), residues: 555 sheet: 0.76 (0.24), residues: 423 loop : -0.89 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.002 0.001 HIS B 410 PHE 0.014 0.001 PHE B 68 TYR 0.019 0.002 TYR A 45 ARG 0.001 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 132 time to evaluate : 1.442 Fit side-chains REVERT: A 341 LEU cc_start: 0.4777 (OUTLIER) cc_final: 0.4491 (mp) REVERT: B 155 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7534 (mt) REVERT: C 155 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7106 (mt) REVERT: C 381 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.6880 (mp) outliers start: 78 outliers final: 45 residues processed: 207 average time/residue: 0.1822 time to fit residues: 61.0086 Evaluate side-chains 176 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 127 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 0.1980 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13335 Z= 0.362 Angle : 0.641 7.686 18108 Z= 0.332 Chirality : 0.047 0.181 2124 Planarity : 0.004 0.031 2400 Dihedral : 4.427 21.133 1893 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 7.10 % Allowed : 28.48 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.18 (0.21), residues: 1743 helix: 1.34 (0.23), residues: 558 sheet: 0.54 (0.24), residues: 423 loop : -1.05 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 173 HIS 0.003 0.001 HIS B 410 PHE 0.022 0.002 PHE B 68 TYR 0.027 0.002 TYR A 45 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 132 time to evaluate : 1.375 Fit side-chains REVERT: A 46 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6686 (tp) REVERT: A 341 LEU cc_start: 0.5017 (OUTLIER) cc_final: 0.4729 (mp) REVERT: B 155 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7627 (mt) REVERT: C 155 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7211 (mt) outliers start: 98 outliers final: 75 residues processed: 225 average time/residue: 0.1946 time to fit residues: 69.6159 Evaluate side-chains 206 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 127 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13335 Z= 0.225 Angle : 0.551 6.582 18108 Z= 0.287 Chirality : 0.044 0.149 2124 Planarity : 0.003 0.026 2400 Dihedral : 4.215 20.250 1893 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.80 % Allowed : 29.78 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.36 (0.21), residues: 1743 helix: 1.59 (0.23), residues: 558 sheet: 0.64 (0.24), residues: 423 loop : -1.03 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.001 0.001 HIS B 409 PHE 0.014 0.001 PHE B 68 TYR 0.028 0.002 TYR C 45 ARG 0.005 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 130 time to evaluate : 1.356 Fit side-chains REVERT: A 341 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4421 (mp) REVERT: B 155 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7508 (mt) REVERT: B 341 LEU cc_start: 0.4927 (OUTLIER) cc_final: 0.4643 (mp) REVERT: C 155 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7103 (mt) REVERT: C 381 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6970 (mp) outliers start: 80 outliers final: 65 residues processed: 206 average time/residue: 0.1803 time to fit residues: 59.4742 Evaluate side-chains 194 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 124 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13335 Z= 0.341 Angle : 0.628 8.298 18108 Z= 0.326 Chirality : 0.047 0.156 2124 Planarity : 0.004 0.029 2400 Dihedral : 4.530 19.555 1893 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 7.10 % Allowed : 28.55 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.11 (0.21), residues: 1743 helix: 1.33 (0.23), residues: 559 sheet: 0.51 (0.24), residues: 423 loop : -1.15 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 173 HIS 0.002 0.001 HIS B 410 PHE 0.023 0.002 PHE B 68 TYR 0.027 0.002 TYR C 45 ARG 0.002 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 130 time to evaluate : 1.499 Fit side-chains REVERT: A 292 ILE cc_start: 0.2142 (OUTLIER) cc_final: 0.1934 (mm) REVERT: A 341 LEU cc_start: 0.4990 (OUTLIER) cc_final: 0.4682 (mp) REVERT: B 155 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7553 (mt) REVERT: B 292 ILE cc_start: 0.2204 (OUTLIER) cc_final: 0.1572 (mm) REVERT: B 341 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4881 (mp) REVERT: C 155 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7189 (mt) REVERT: C 292 ILE cc_start: 0.2206 (OUTLIER) cc_final: 0.1829 (mm) outliers start: 98 outliers final: 82 residues processed: 222 average time/residue: 0.1834 time to fit residues: 65.3243 Evaluate side-chains 217 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 128 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13335 Z= 0.242 Angle : 0.567 7.802 18108 Z= 0.295 Chirality : 0.045 0.154 2124 Planarity : 0.003 0.027 2400 Dihedral : 4.341 19.344 1893 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.88 % Allowed : 29.13 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.25 (0.21), residues: 1743 helix: 1.54 (0.23), residues: 559 sheet: 0.58 (0.25), residues: 423 loop : -1.13 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 173 HIS 0.001 0.001 HIS B 409 PHE 0.016 0.001 PHE B 68 TYR 0.026 0.002 TYR C 45 ARG 0.006 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 135 time to evaluate : 1.562 Fit side-chains REVERT: A 292 ILE cc_start: 0.2082 (OUTLIER) cc_final: 0.1870 (mm) REVERT: A 341 LEU cc_start: 0.4850 (OUTLIER) cc_final: 0.4588 (mp) REVERT: B 155 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 292 ILE cc_start: 0.1935 (OUTLIER) cc_final: 0.1301 (mm) REVERT: B 341 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4716 (mp) REVERT: B 387 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7436 (mp) REVERT: C 155 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7125 (mt) REVERT: C 292 ILE cc_start: 0.2151 (OUTLIER) cc_final: 0.1760 (mm) outliers start: 95 outliers final: 80 residues processed: 224 average time/residue: 0.1924 time to fit residues: 68.2224 Evaluate side-chains 219 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 131 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 30.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13335 Z= 0.199 Angle : 0.548 7.963 18108 Z= 0.285 Chirality : 0.044 0.137 2124 Planarity : 0.003 0.027 2400 Dihedral : 4.155 21.313 1893 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.16 % Allowed : 29.93 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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 (0.21), residues: 1743 helix: 1.82 (0.23), residues: 549 sheet: 0.69 (0.25), residues: 423 loop : -1.01 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.001 0.000 HIS B 409 PHE 0.011 0.001 PHE B 68 TYR 0.028 0.002 TYR C 454 ARG 0.007 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 136 time to evaluate : 1.446 Fit side-chains REVERT: A 341 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4533 (mp) REVERT: B 155 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7446 (mt) REVERT: B 341 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4781 (mp) REVERT: B 387 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7463 (mp) REVERT: C 155 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7079 (mt) REVERT: C 292 ILE cc_start: 0.2101 (OUTLIER) cc_final: 0.1750 (mm) REVERT: C 381 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.6956 (mp) REVERT: C 387 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7525 (mp) REVERT: C 535 ASP cc_start: 0.5494 (t0) cc_final: 0.5246 (t0) outliers start: 85 outliers final: 70 residues processed: 216 average time/residue: 0.1874 time to fit residues: 64.7407 Evaluate side-chains 209 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 131 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 155 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13335 Z= 0.252 Angle : 0.581 9.495 18108 Z= 0.301 Chirality : 0.045 0.149 2124 Planarity : 0.004 0.031 2400 Dihedral : 4.256 21.290 1893 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 6.74 % Allowed : 29.20 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.40 (0.21), residues: 1743 helix: 1.73 (0.23), residues: 548 sheet: 0.66 (0.25), residues: 423 loop : -1.06 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS C 410 PHE 0.015 0.001 PHE B 68 TYR 0.026 0.002 TYR C 454 ARG 0.007 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 133 time to evaluate : 1.448 Fit side-chains REVERT: A 292 ILE cc_start: 0.1971 (OUTLIER) cc_final: 0.1702 (mm) REVERT: A 341 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4453 (mp) REVERT: B 155 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7531 (mt) REVERT: B 341 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4773 (mp) REVERT: B 387 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7416 (mp) REVERT: C 155 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7087 (mt) REVERT: C 292 ILE cc_start: 0.2228 (OUTLIER) cc_final: 0.1872 (mm) REVERT: C 381 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.6991 (mp) REVERT: C 387 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7609 (mp) outliers start: 93 outliers final: 81 residues processed: 220 average time/residue: 0.1852 time to fit residues: 65.9301 Evaluate side-chains 220 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 130 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 159 optimal weight: 0.3980 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13335 Z= 0.261 Angle : 0.593 9.707 18108 Z= 0.308 Chirality : 0.045 0.153 2124 Planarity : 0.004 0.030 2400 Dihedral : 4.305 21.024 1893 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.88 % Allowed : 29.20 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.36 (0.21), residues: 1743 helix: 1.68 (0.23), residues: 550 sheet: 0.64 (0.25), residues: 423 loop : -1.08 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 173 HIS 0.002 0.001 HIS C 410 PHE 0.016 0.001 PHE B 68 TYR 0.034 0.002 TYR C 454 ARG 0.007 0.000 ARG B 329 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 131 time to evaluate : 1.571 Fit side-chains REVERT: A 216 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8261 (mp) REVERT: A 292 ILE cc_start: 0.1943 (OUTLIER) cc_final: 0.1658 (mm) REVERT: A 341 LEU cc_start: 0.4758 (OUTLIER) cc_final: 0.4438 (mp) REVERT: B 27 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7833 (mm) REVERT: B 155 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7536 (mt) REVERT: B 275 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.5305 (m-10) REVERT: B 292 ILE cc_start: 0.1942 (OUTLIER) cc_final: 0.1301 (mm) REVERT: B 341 LEU cc_start: 0.5067 (OUTLIER) cc_final: 0.4789 (mp) REVERT: B 387 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7477 (mp) REVERT: C 155 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7099 (mt) REVERT: C 292 ILE cc_start: 0.2231 (OUTLIER) cc_final: 0.1892 (mm) REVERT: C 381 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.6998 (mt) REVERT: C 387 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7553 (mp) outliers start: 95 outliers final: 81 residues processed: 220 average time/residue: 0.1875 time to fit residues: 66.1889 Evaluate side-chains 226 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 132 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 580 MET Chi-restraints excluded: chain C residue 584 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 0.0570 chunk 121 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.218980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.175616 restraints weight = 19007.435| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 3.58 r_work: 0.4327 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13335 Z= 0.282 Angle : 0.609 10.481 18108 Z= 0.315 Chirality : 0.046 0.185 2124 Planarity : 0.004 0.028 2400 Dihedral : 4.388 20.782 1893 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 7.25 % Allowed : 28.99 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.18 % 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: 0.28 (0.21), residues: 1743 helix: 1.58 (0.23), residues: 550 sheet: 0.59 (0.25), residues: 423 loop : -1.09 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 173 HIS 0.002 0.001 HIS C 410 PHE 0.018 0.002 PHE B 68 TYR 0.040 0.002 TYR C 454 ARG 0.007 0.000 ARG B 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.02 seconds wall clock time: 48 minutes 33.43 seconds (2913.43 seconds total)