Starting phenix.real_space_refine on Fri Jul 19 20:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tss_41600/07_2024/8tss_41600.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tss_41600/07_2024/8tss_41600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tss_41600/07_2024/8tss_41600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tss_41600/07_2024/8tss_41600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tss_41600/07_2024/8tss_41600.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tss_41600/07_2024/8tss_41600.cif" } resolution = 3.7 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= 0.001 sd= 0.042 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 54 5.16 5 C 5652 2.51 5 N 1552 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B ASP 329": "OD1" <-> "OD2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 498": "OD1" <-> "OD2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 552": "OE1" <-> "OE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4459 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 13, 'TRANS': 561} Chain: "B" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4459 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 13, 'TRANS': 561} Time building chain proxies: 5.01, per 1000 atoms: 0.56 Number of scatterers: 8918 At special positions: 0 Unit cell: (67.095, 135.255, 136.32, 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 54 16.00 O 1660 8.00 N 1552 7.00 C 5652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 70.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 48 removed outlier: 3.692A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 66 through 109 Processing helix chain 'A' and resid 112 through 119 removed outlier: 4.322A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 164 removed outlier: 4.029A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 209 removed outlier: 3.715A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 4.020A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.787A pdb=" N LEU A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 272 removed outlier: 4.439A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 275 through 280 removed outlier: 5.710A pdb=" N THR A 280 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 323 removed outlier: 4.064A pdb=" N THR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.587A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.584A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.750A pdb=" N ALA A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 482 through 497 Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 538 through 545 removed outlier: 3.781A pdb=" N ILE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 578 removed outlier: 3.652A pdb=" N MET A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 21 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 53 removed outlier: 3.695A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 66 through 109 Processing helix chain 'B' and resid 112 through 119 removed outlier: 4.234A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 164 removed outlier: 4.001A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 209 Proline residue: B 176 - end of helix removed outlier: 4.029A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.551A pdb=" N LEU B 218 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 272 removed outlier: 4.328A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.579A pdb=" N ASP B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 323 removed outlier: 4.084A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.568A pdb=" N THR B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.703A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.871A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.569A pdb=" N ASN B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 482 through 497 removed outlier: 3.529A pdb=" N ARG B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.626A pdb=" N ILE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.738A pdb=" N MET B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 365 removed outlier: 5.540A pdb=" N VAL A 347 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN A 363 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG A 345 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS A 365 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 343 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 423 removed outlier: 6.494A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP A 505 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 422 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A 375 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU A 552 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 365 removed outlier: 5.524A pdb=" N VAL B 347 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN B 363 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG B 345 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 365 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU B 343 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU B 399 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 423 removed outlier: 6.805A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASP B 505 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 422 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 558 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU B 552 " --> pdb=" O ILE B 556 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) 575 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2956 1.35 - 1.46: 1945 1.46 - 1.58: 4045 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 9050 Sorted by residual: bond pdb=" N LEU A 279 " pdb=" CA LEU A 279 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.16e+00 bond pdb=" N ILE A 389 " pdb=" CA ILE A 389 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.15e+00 bond pdb=" N SER A 278 " pdb=" CA SER A 278 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.10e-02 8.26e+03 6.93e+00 bond pdb=" N LEU A 388 " pdb=" CA LEU A 388 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.91e+00 bond pdb=" N SER A 387 " pdb=" CA SER A 387 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.91e+00 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.48: 127 105.48 - 112.62: 4911 112.62 - 119.76: 2949 119.76 - 126.89: 4182 126.89 - 134.03: 61 Bond angle restraints: 12230 Sorted by residual: angle pdb=" CA ARG B 190 " pdb=" CB ARG B 190 " pdb=" CG ARG B 190 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CB MET A 276 " pdb=" CG MET A 276 " pdb=" SD MET A 276 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET A 100 " pdb=" CG MET A 100 " pdb=" SD MET A 100 " ideal model delta sigma weight residual 112.70 123.64 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CB MET B 100 " pdb=" CG MET B 100 " pdb=" SD MET B 100 " ideal model delta sigma weight residual 112.70 123.44 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CB MET B 456 " pdb=" CG MET B 456 " pdb=" SD MET B 456 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 4594 14.05 - 28.11: 598 28.11 - 42.16: 228 42.16 - 56.21: 47 56.21 - 70.26: 37 Dihedral angle restraints: 5504 sinusoidal: 2182 harmonic: 3322 Sorted by residual: dihedral pdb=" CA GLN B 209 " pdb=" C GLN B 209 " pdb=" N MET B 210 " pdb=" CA MET B 210 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA THR A 199 " pdb=" C THR A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER A 251 " pdb=" C SER A 251 " pdb=" N ASP A 252 " pdb=" CA ASP A 252 " ideal model delta harmonic sigma weight residual 180.00 -163.92 -16.08 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 5501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1058 0.042 - 0.084: 289 0.084 - 0.127: 94 0.127 - 0.169: 11 0.169 - 0.211: 2 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CA ILE A 389 " pdb=" N ILE A 389 " pdb=" C ILE A 389 " pdb=" CB ILE A 389 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 375 " pdb=" CA VAL B 375 " pdb=" CG1 VAL B 375 " pdb=" CG2 VAL B 375 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CG LEU B 279 " pdb=" CB LEU B 279 " pdb=" CD1 LEU B 279 " pdb=" CD2 LEU B 279 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1451 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 111 " -0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO A 112 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 272 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO B 273 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 499 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO B 500 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " 0.030 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1837 2.78 - 3.31: 9610 3.31 - 3.84: 15224 3.84 - 4.37: 16731 4.37 - 4.90: 28103 Nonbonded interactions: 71505 Sorted by model distance: nonbonded pdb=" O ASP A 467 " pdb=" OG1 THR A 472 " model vdw 2.244 2.440 nonbonded pdb=" O LEU A 526 " pdb=" NH1 ARG A 530 " model vdw 2.256 2.520 nonbonded pdb=" O LEU B 526 " pdb=" NH1 ARG B 530 " model vdw 2.261 2.520 nonbonded pdb=" OG SER B 380 " pdb=" OE1 GLU B 552 " model vdw 2.268 2.440 nonbonded pdb=" ND1 HIS B 562 " pdb=" OH TYR B 572 " model vdw 2.271 2.520 ... (remaining 71500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.020 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.940 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 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 : 0.004 0.056 9050 Z= 0.241 Angle : 0.750 11.275 12230 Z= 0.399 Chirality : 0.043 0.211 1454 Planarity : 0.006 0.077 1548 Dihedral : 15.891 70.263 3356 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 0.41 % Allowed : 23.93 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1146 helix: 0.91 (0.19), residues: 728 sheet: 0.15 (0.77), residues: 54 loop : -1.14 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 66 HIS 0.015 0.001 HIS A 214 PHE 0.026 0.002 PHE A 116 TYR 0.019 0.001 TYR B 439 ARG 0.014 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7530 (t70) cc_final: 0.7271 (t70) REVERT: B 107 HIS cc_start: 0.7834 (t70) cc_final: 0.7464 (t70) REVERT: B 210 MET cc_start: 0.6669 (mtm) cc_final: 0.6283 (mtm) outliers start: 4 outliers final: 3 residues processed: 138 average time/residue: 0.1984 time to fit residues: 39.1332 Evaluate side-chains 129 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.0370 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.190 Angle : 0.591 8.124 12230 Z= 0.306 Chirality : 0.041 0.146 1454 Planarity : 0.005 0.059 1548 Dihedral : 4.555 50.861 1257 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.78 % Allowed : 21.06 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1146 helix: 1.42 (0.19), residues: 760 sheet: 0.36 (0.76), residues: 54 loop : -1.30 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 66 HIS 0.017 0.001 HIS A 214 PHE 0.014 0.002 PHE B 13 TYR 0.015 0.001 TYR B 439 ARG 0.007 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7731 (t70) cc_final: 0.7492 (t70) REVERT: A 408 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7570 (mpt180) REVERT: A 578 MET cc_start: 0.5368 (pmm) cc_final: 0.4996 (pmm) REVERT: B 107 HIS cc_start: 0.8017 (t70) cc_final: 0.7746 (t70) REVERT: B 210 MET cc_start: 0.6349 (mtm) cc_final: 0.6127 (mtm) REVERT: B 322 LEU cc_start: 0.8312 (tp) cc_final: 0.8079 (tt) outliers start: 37 outliers final: 16 residues processed: 170 average time/residue: 0.1946 time to fit residues: 46.5277 Evaluate side-chains 149 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9050 Z= 0.278 Angle : 0.639 7.605 12230 Z= 0.330 Chirality : 0.042 0.168 1454 Planarity : 0.004 0.060 1548 Dihedral : 3.898 18.895 1250 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.13 % Allowed : 20.45 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1146 helix: 1.42 (0.19), residues: 756 sheet: 0.38 (0.73), residues: 54 loop : -1.35 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 66 HIS 0.011 0.001 HIS A 214 PHE 0.021 0.002 PHE A 429 TYR 0.020 0.002 TYR A 268 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 139 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 107 HIS cc_start: 0.7945 (t70) cc_final: 0.7612 (t70) REVERT: A 309 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6411 (tt0) REVERT: A 388 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8888 (tp) REVERT: A 578 MET cc_start: 0.5641 (pmm) cc_final: 0.5329 (pmm) REVERT: B 107 HIS cc_start: 0.8179 (t70) cc_final: 0.7821 (t70) REVERT: B 250 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 309 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6239 (tt0) REVERT: B 395 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5876 (tp) REVERT: B 578 MET cc_start: 0.4424 (pmm) cc_final: 0.4169 (pmm) outliers start: 60 outliers final: 34 residues processed: 180 average time/residue: 0.1772 time to fit residues: 46.0212 Evaluate side-chains 166 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9050 Z= 0.249 Angle : 0.625 8.027 12230 Z= 0.318 Chirality : 0.042 0.154 1454 Planarity : 0.004 0.046 1548 Dihedral : 3.892 18.422 1250 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.32 % Allowed : 21.88 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1146 helix: 1.48 (0.19), residues: 746 sheet: 0.51 (0.79), residues: 44 loop : -1.20 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 66 HIS 0.012 0.001 HIS A 214 PHE 0.024 0.002 PHE A 429 TYR 0.018 0.002 TYR B 268 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 130 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 107 HIS cc_start: 0.7944 (t70) cc_final: 0.7582 (t70) REVERT: A 196 MET cc_start: 0.5663 (tpp) cc_final: 0.5337 (tpp) REVERT: A 309 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: A 388 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 107 HIS cc_start: 0.8127 (t70) cc_final: 0.7807 (t70) REVERT: B 250 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7782 (tp) REVERT: B 309 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6174 (tt0) REVERT: B 578 MET cc_start: 0.4545 (pmm) cc_final: 0.4317 (pmm) outliers start: 52 outliers final: 38 residues processed: 171 average time/residue: 0.1746 time to fit residues: 43.4134 Evaluate side-chains 170 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.167 Angle : 0.586 10.669 12230 Z= 0.292 Chirality : 0.040 0.134 1454 Planarity : 0.004 0.042 1548 Dihedral : 3.758 19.518 1250 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.09 % Allowed : 22.49 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1146 helix: 1.65 (0.19), residues: 750 sheet: 0.73 (0.78), residues: 44 loop : -1.11 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 66 HIS 0.007 0.001 HIS A 214 PHE 0.018 0.001 PHE A 429 TYR 0.019 0.001 TYR B 130 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7774 (t70) cc_final: 0.7477 (t70) REVERT: A 203 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.5997 (t) REVERT: A 242 MET cc_start: 0.7540 (mmt) cc_final: 0.7148 (mmt) REVERT: B 107 HIS cc_start: 0.8034 (t70) cc_final: 0.7780 (t70) REVERT: B 395 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5690 (tp) REVERT: B 466 MET cc_start: 0.8617 (mmm) cc_final: 0.8230 (mmm) outliers start: 40 outliers final: 28 residues processed: 169 average time/residue: 0.1705 time to fit residues: 41.8082 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.198 Angle : 0.595 9.702 12230 Z= 0.299 Chirality : 0.040 0.164 1454 Planarity : 0.004 0.039 1548 Dihedral : 3.783 22.084 1250 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.42 % Allowed : 21.78 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1146 helix: 1.67 (0.19), residues: 748 sheet: 0.97 (0.78), residues: 44 loop : -1.12 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 66 HIS 0.008 0.001 HIS A 214 PHE 0.017 0.002 PHE A 429 TYR 0.018 0.001 TYR B 268 ARG 0.008 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 135 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7845 (t70) cc_final: 0.7535 (t70) REVERT: A 203 VAL cc_start: 0.5937 (OUTLIER) cc_final: 0.5588 (t) REVERT: A 242 MET cc_start: 0.7468 (mmt) cc_final: 0.7145 (mmt) REVERT: A 309 GLN cc_start: 0.6690 (OUTLIER) cc_final: 0.6238 (tt0) REVERT: B 107 HIS cc_start: 0.8021 (t70) cc_final: 0.7753 (t70) REVERT: B 125 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6605 (tp) REVERT: B 332 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7984 (mmtt) REVERT: B 395 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5762 (tp) REVERT: B 429 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.6083 (p90) REVERT: B 466 MET cc_start: 0.8638 (mmm) cc_final: 0.8216 (mmm) outliers start: 53 outliers final: 37 residues processed: 172 average time/residue: 0.1818 time to fit residues: 45.0158 Evaluate side-chains 171 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 67 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.183 Angle : 0.596 11.022 12230 Z= 0.296 Chirality : 0.040 0.138 1454 Planarity : 0.004 0.043 1548 Dihedral : 3.750 19.883 1250 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.21 % Allowed : 22.29 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1146 helix: 1.71 (0.19), residues: 750 sheet: 1.17 (0.79), residues: 44 loop : -1.08 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 66 HIS 0.007 0.001 HIS A 214 PHE 0.017 0.001 PHE A 429 TYR 0.016 0.001 TYR B 268 ARG 0.011 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7819 (t70) cc_final: 0.7536 (t70) REVERT: A 190 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7282 (mtm-85) REVERT: A 203 VAL cc_start: 0.5859 (OUTLIER) cc_final: 0.5538 (t) REVERT: A 309 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6232 (tt0) REVERT: B 125 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6513 (tp) REVERT: B 309 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6215 (tt0) REVERT: B 332 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7939 (mmtt) REVERT: B 395 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5762 (tp) REVERT: B 429 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6181 (p90) REVERT: B 466 MET cc_start: 0.8581 (mmm) cc_final: 0.8172 (mmm) outliers start: 51 outliers final: 39 residues processed: 171 average time/residue: 0.1757 time to fit residues: 43.7451 Evaluate side-chains 173 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.191 Angle : 0.595 9.627 12230 Z= 0.297 Chirality : 0.040 0.133 1454 Planarity : 0.004 0.038 1548 Dihedral : 3.787 22.311 1250 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.52 % Allowed : 21.98 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1146 helix: 1.70 (0.19), residues: 750 sheet: 1.34 (0.79), residues: 44 loop : -1.05 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 66 HIS 0.007 0.001 HIS A 214 PHE 0.021 0.002 PHE A 56 TYR 0.011 0.001 TYR B 439 ARG 0.008 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 128 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7892 (t70) cc_final: 0.7552 (t70) REVERT: A 196 MET cc_start: 0.5398 (tpp) cc_final: 0.4968 (tpp) REVERT: A 203 VAL cc_start: 0.5809 (OUTLIER) cc_final: 0.5516 (t) REVERT: A 242 MET cc_start: 0.7405 (mmt) cc_final: 0.7077 (mmt) REVERT: A 309 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: A 322 LEU cc_start: 0.8329 (tp) cc_final: 0.8084 (tt) REVERT: A 465 LYS cc_start: 0.8931 (tttt) cc_final: 0.8510 (pttm) REVERT: B 125 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6577 (tp) REVERT: B 309 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: B 332 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7968 (mmtt) REVERT: B 395 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5602 (tp) REVERT: B 429 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5723 (p90) REVERT: B 466 MET cc_start: 0.8609 (mmm) cc_final: 0.8158 (mmm) outliers start: 54 outliers final: 42 residues processed: 169 average time/residue: 0.1644 time to fit residues: 40.8606 Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9050 Z= 0.238 Angle : 0.629 11.220 12230 Z= 0.314 Chirality : 0.041 0.183 1454 Planarity : 0.004 0.038 1548 Dihedral : 3.837 21.006 1250 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 5.93 % Allowed : 21.88 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1146 helix: 1.63 (0.19), residues: 746 sheet: 1.56 (0.83), residues: 44 loop : -1.08 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 66 HIS 0.007 0.001 HIS A 214 PHE 0.021 0.002 PHE B 429 TYR 0.018 0.001 TYR B 439 ARG 0.010 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 132 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7952 (t70) cc_final: 0.7598 (t70) REVERT: A 125 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6647 (tp) REVERT: A 190 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7403 (mtm-85) REVERT: A 196 MET cc_start: 0.5410 (tpp) cc_final: 0.5065 (tpp) REVERT: A 203 VAL cc_start: 0.5791 (OUTLIER) cc_final: 0.5511 (t) REVERT: A 309 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6345 (tt0) REVERT: A 322 LEU cc_start: 0.8424 (tp) cc_final: 0.8206 (tt) REVERT: A 465 LYS cc_start: 0.8914 (tttt) cc_final: 0.8504 (pttm) REVERT: B 125 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6550 (tp) REVERT: B 196 MET cc_start: 0.5319 (tpp) cc_final: 0.4198 (tpp) REVERT: B 309 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.6337 (tt0) REVERT: B 395 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5649 (tp) REVERT: B 429 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.5880 (p90) REVERT: B 435 ASN cc_start: 0.5283 (m-40) cc_final: 0.5064 (t0) REVERT: B 466 MET cc_start: 0.8567 (mmm) cc_final: 0.8167 (mmm) outliers start: 58 outliers final: 46 residues processed: 177 average time/residue: 0.1728 time to fit residues: 44.9580 Evaluate side-chains 181 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.184 Angle : 0.600 10.050 12230 Z= 0.299 Chirality : 0.040 0.182 1454 Planarity : 0.004 0.038 1548 Dihedral : 3.798 20.624 1250 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 4.91 % Allowed : 23.21 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1146 helix: 1.67 (0.19), residues: 756 sheet: 3.25 (1.15), residues: 24 loop : -1.17 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.008 0.001 HIS A 214 PHE 0.020 0.002 PHE A 56 TYR 0.014 0.001 TYR B 439 ARG 0.010 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 129 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7873 (t70) cc_final: 0.7548 (t70) REVERT: A 125 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6607 (tp) REVERT: A 190 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7406 (mtm-85) REVERT: A 196 MET cc_start: 0.5369 (tpp) cc_final: 0.5107 (tpp) REVERT: A 203 VAL cc_start: 0.5639 (OUTLIER) cc_final: 0.5388 (t) REVERT: A 242 MET cc_start: 0.7421 (mmt) cc_final: 0.7112 (mmt) REVERT: A 309 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: A 322 LEU cc_start: 0.8378 (tp) cc_final: 0.8164 (tt) REVERT: A 465 LYS cc_start: 0.8898 (tttt) cc_final: 0.8520 (pttp) REVERT: B 125 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6519 (tp) REVERT: B 196 MET cc_start: 0.5166 (tpp) cc_final: 0.4769 (tpp) REVERT: B 200 MET cc_start: 0.5490 (mpp) cc_final: 0.5077 (mpt) REVERT: B 309 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6309 (tt0) REVERT: B 395 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5593 (tp) REVERT: B 429 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5627 (p90) REVERT: B 466 MET cc_start: 0.8509 (mmm) cc_final: 0.8106 (mmm) outliers start: 48 outliers final: 39 residues processed: 167 average time/residue: 0.1639 time to fit residues: 40.5866 Evaluate side-chains 173 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 GLN Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** 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 = 0.4388 r_free = 0.4388 target = 0.204989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.152655 restraints weight = 11241.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150023 restraints weight = 13681.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.152658 restraints weight = 10928.803| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9050 Z= 0.202 Angle : 0.602 9.831 12230 Z= 0.302 Chirality : 0.040 0.181 1454 Planarity : 0.004 0.038 1548 Dihedral : 3.799 20.529 1250 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 5.11 % Allowed : 23.62 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1146 helix: 1.64 (0.19), residues: 756 sheet: 3.18 (1.12), residues: 24 loop : -1.15 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 66 HIS 0.008 0.001 HIS A 214 PHE 0.020 0.002 PHE A 56 TYR 0.015 0.001 TYR B 439 ARG 0.010 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.27 seconds wall clock time: 32 minutes 18.26 seconds (1938.26 seconds total)