Starting phenix.real_space_refine on Thu Feb 13 10:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tss_41600/02_2025/8tss_41600.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tss_41600/02_2025/8tss_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/cci-nas-00/data/ceres_data/8tss_41600/02_2025/8tss_41600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tss_41600/02_2025/8tss_41600.map" model { file = "/net/cci-nas-00/data/ceres_data/8tss_41600/02_2025/8tss_41600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tss_41600/02_2025/8tss_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. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.49, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 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: 0.95 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: 2.57 Time building geometry restraints manager: 2.76 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: 0.00 - 2.25: 12005 2.25 - 4.51: 181 4.51 - 6.76: 31 6.76 - 9.02: 5 9.02 - 11.27: 8 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 3.040 nonbonded pdb=" O LEU A 526 " pdb=" NH1 ARG A 530 " model vdw 2.256 3.120 nonbonded pdb=" O LEU B 526 " pdb=" NH1 ARG B 530 " model vdw 2.261 3.120 nonbonded pdb=" OG SER B 380 " pdb=" OE1 GLU B 552 " model vdw 2.268 3.040 nonbonded pdb=" ND1 HIS B 562 " pdb=" OH TYR B 572 " model vdw 2.271 3.120 ... (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 Time spend for trying shortcut: 0.05 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.970 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.981 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: 0.2017 time to fit residues: 39.3494 Evaluate side-chains 129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 0.7980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 537 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 = 0.4235 r_free = 0.4235 target = 0.195211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138028 restraints weight = 10877.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140140 restraints weight = 6577.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141265 restraints weight = 5386.692| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.207 Angle : 0.611 8.032 12230 Z= 0.318 Chirality : 0.041 0.149 1454 Planarity : 0.005 0.059 1548 Dihedral : 4.605 50.914 1257 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.29 % Allowed : 20.45 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1146 helix: 1.40 (0.19), residues: 754 sheet: 0.17 (0.75), residues: 54 loop : -1.32 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 66 HIS 0.018 0.002 HIS A 214 PHE 0.015 0.002 PHE B 429 TYR 0.011 0.001 TYR B 439 ARG 0.006 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 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7957 (t70) cc_final: 0.7558 (t70) REVERT: A 408 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7960 (mpt180) REVERT: A 578 MET cc_start: 0.6144 (pmm) cc_final: 0.5896 (pmm) REVERT: B 107 HIS cc_start: 0.8116 (t70) cc_final: 0.7724 (t70) outliers start: 42 outliers final: 20 residues processed: 174 average time/residue: 0.2003 time to fit residues: 49.0200 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 92 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 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 501 ILE Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain B residue 123 THR 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 301 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 389 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 2 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 HIS B 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.190178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131697 restraints weight = 11206.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133863 restraints weight = 7677.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134401 restraints weight = 6404.383| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1905 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= 0.281 Angle : 0.661 7.639 12230 Z= 0.340 Chirality : 0.043 0.174 1454 Planarity : 0.004 0.055 1548 Dihedral : 3.922 21.201 1250 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.13 % Allowed : 19.73 % Favored : 74.13 % 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: 0.74 (0.25), residues: 1146 helix: 1.31 (0.19), residues: 762 sheet: 0.39 (0.79), residues: 44 loop : -1.36 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 66 HIS 0.012 0.001 HIS A 214 PHE 0.024 0.002 PHE B 429 TYR 0.014 0.002 TYR A 439 ARG 0.009 0.000 ARG B 538 *********************** 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 201 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 141 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7874 (mm) REVERT: A 107 HIS cc_start: 0.8110 (t70) cc_final: 0.7564 (t70) REVERT: A 309 GLN cc_start: 0.6484 (OUTLIER) cc_final: 0.6158 (tt0) REVERT: A 578 MET cc_start: 0.6367 (pmm) cc_final: 0.6154 (pmm) REVERT: B 107 HIS cc_start: 0.8195 (t70) cc_final: 0.7733 (t70) REVERT: B 250 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.7193 (tp) REVERT: B 309 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.6061 (tt0) REVERT: B 395 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.5840 (tp) REVERT: B 460 MET cc_start: 0.7050 (mmm) cc_final: 0.6760 (mmm) REVERT: B 495 LEU cc_start: 0.8804 (mm) cc_final: 0.8499 (mm) REVERT: B 537 HIS cc_start: 0.6229 (t-170) cc_final: 0.5889 (t-170) REVERT: B 578 MET cc_start: 0.5221 (pmm) cc_final: 0.4895 (pmm) outliers start: 60 outliers final: 37 residues processed: 182 average time/residue: 0.1754 time to fit residues: 46.6165 Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 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 375 VAL 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 203 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 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 chunk 78 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.206499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152841 restraints weight = 11212.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152045 restraints weight = 11710.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154472 restraints weight = 8446.228| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9050 Z= 0.189 Angle : 0.592 8.723 12230 Z= 0.303 Chirality : 0.041 0.136 1454 Planarity : 0.004 0.045 1548 Dihedral : 3.841 21.110 1250 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.60 % Allowed : 22.90 % 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: 1.01 (0.25), residues: 1146 helix: 1.53 (0.19), residues: 750 sheet: 0.29 (0.78), residues: 44 loop : -1.15 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 66 HIS 0.009 0.001 HIS A 214 PHE 0.024 0.002 PHE A 429 TYR 0.018 0.001 TYR A 130 ARG 0.003 0.000 ARG A 493 *********************** 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 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7955 (t70) cc_final: 0.7605 (t70) REVERT: A 203 VAL cc_start: 0.6267 (OUTLIER) cc_final: 0.5987 (t) REVERT: A 216 GLU cc_start: 0.8483 (tp30) cc_final: 0.8211 (tp30) REVERT: A 309 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6080 (tt0) REVERT: B 107 HIS cc_start: 0.8080 (t70) cc_final: 0.7725 (t70) REVERT: B 309 GLN cc_start: 0.6575 (OUTLIER) cc_final: 0.6082 (tt0) REVERT: B 335 ILE cc_start: 0.8771 (tp) cc_final: 0.8206 (pt) REVERT: B 466 MET cc_start: 0.8570 (mmm) cc_final: 0.8010 (mmm) REVERT: B 495 LEU cc_start: 0.8670 (mm) cc_final: 0.8381 (mm) REVERT: B 537 HIS cc_start: 0.6166 (t-170) cc_final: 0.5931 (t-170) REVERT: B 578 MET cc_start: 0.5076 (pmm) cc_final: 0.4842 (pmm) outliers start: 45 outliers final: 29 residues processed: 174 average time/residue: 0.1739 time to fit residues: 43.8574 Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 92 VAL 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 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 324 SER 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 562 HIS Chi-restraints excluded: chain B residue 92 VAL 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 245 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 309 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 THR 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 26 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.202791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.149677 restraints weight = 11152.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.148583 restraints weight = 11263.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150722 restraints weight = 9157.636| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9050 Z= 0.230 Angle : 0.625 10.289 12230 Z= 0.318 Chirality : 0.041 0.134 1454 Planarity : 0.004 0.057 1548 Dihedral : 3.910 22.553 1250 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.83 % Allowed : 21.68 % 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: 1.00 (0.25), residues: 1146 helix: 1.55 (0.19), residues: 746 sheet: 0.25 (0.77), 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 0.006 0.001 HIS A 107 PHE 0.025 0.002 PHE A 429 TYR 0.020 0.001 TYR B 130 ARG 0.014 0.000 ARG B 61 *********************** 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 198 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.8040 (t70) cc_final: 0.7625 (t70) REVERT: A 216 GLU cc_start: 0.8506 (tp30) cc_final: 0.8265 (tp30) REVERT: A 309 GLN cc_start: 0.6648 (OUTLIER) cc_final: 0.6171 (tt0) REVERT: A 495 LEU cc_start: 0.8653 (mm) cc_final: 0.8405 (mm) REVERT: B 107 HIS cc_start: 0.8200 (t70) cc_final: 0.7864 (t70) REVERT: B 125 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6055 (tp) REVERT: B 309 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6126 (tt0) REVERT: B 332 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8226 (mmtt) REVERT: B 335 ILE cc_start: 0.8720 (tp) cc_final: 0.8467 (pt) REVERT: B 395 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.5844 (tp) REVERT: B 435 ASN cc_start: 0.5424 (m-40) cc_final: 0.5136 (t0) REVERT: B 466 MET cc_start: 0.8639 (mmm) cc_final: 0.8010 (mmm) REVERT: B 495 LEU cc_start: 0.8709 (mm) cc_final: 0.8435 (mm) REVERT: B 578 MET cc_start: 0.5330 (pmm) cc_final: 0.5082 (pmm) outliers start: 57 outliers final: 45 residues processed: 183 average time/residue: 0.1748 time to fit residues: 46.9817 Evaluate side-chains 179 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 123 THR 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 324 SER Chi-restraints excluded: chain A residue 329 ASP 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 562 HIS Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 40 SER 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 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 245 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 320 THR 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 389 ILE 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 Chi-restraints excluded: chain B residue 562 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.202987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.149296 restraints weight = 11182.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.148112 restraints weight = 12163.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150590 restraints weight = 9187.965| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9050 Z= 0.230 Angle : 0.620 8.961 12230 Z= 0.318 Chirality : 0.041 0.134 1454 Planarity : 0.004 0.040 1548 Dihedral : 3.918 21.590 1250 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.65 % Allowed : 21.88 % Favored : 71.47 % 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: 1.04 (0.25), residues: 1146 helix: 1.54 (0.19), residues: 748 sheet: 0.32 (0.77), residues: 44 loop : -1.11 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 66 HIS 0.005 0.001 HIS A 107 PHE 0.026 0.002 PHE A 429 TYR 0.021 0.001 TYR B 268 ARG 0.007 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 198 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.8047 (t70) cc_final: 0.7591 (t70) REVERT: A 190 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8082 (mtm-85) REVERT: A 216 GLU cc_start: 0.8523 (tp30) cc_final: 0.8308 (tp30) REVERT: A 309 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6278 (tt0) REVERT: A 495 LEU cc_start: 0.8657 (mm) cc_final: 0.8396 (mm) REVERT: B 125 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6042 (tp) REVERT: B 250 ILE cc_start: 0.7908 (tp) cc_final: 0.7672 (tp) REVERT: B 309 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6160 (tt0) REVERT: B 395 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.5710 (tp) REVERT: B 429 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6442 (p90) REVERT: B 466 MET cc_start: 0.8593 (mmm) cc_final: 0.7986 (mmm) REVERT: B 578 MET cc_start: 0.5462 (pmm) cc_final: 0.5107 (pmm) outliers start: 65 outliers final: 49 residues processed: 180 average time/residue: 0.1715 time to fit residues: 45.0240 Evaluate side-chains 181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 127 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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 324 SER Chi-restraints excluded: chain A residue 362 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 562 HIS Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 40 SER 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 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 245 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 320 THR Chi-restraints excluded: chain B residue 362 ILE 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 426 VAL Chi-restraints excluded: chain B residue 429 PHE 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 25 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 HIS B 427 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.199714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147182 restraints weight = 11396.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143735 restraints weight = 12875.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.146242 restraints weight = 9802.364| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9050 Z= 0.297 Angle : 0.671 9.754 12230 Z= 0.343 Chirality : 0.043 0.170 1454 Planarity : 0.004 0.040 1548 Dihedral : 4.046 24.093 1250 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.67 % Allowed : 21.57 % Favored : 70.76 % 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: 0.87 (0.24), residues: 1146 helix: 1.39 (0.19), residues: 746 sheet: 0.43 (0.78), residues: 44 loop : -1.12 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 66 HIS 0.006 0.001 HIS A 107 PHE 0.028 0.002 PHE A 429 TYR 0.022 0.002 TYR B 268 ARG 0.004 0.000 ARG A 102 *********************** 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 202 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 127 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.8105 (t70) cc_final: 0.7629 (t70) REVERT: A 125 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6065 (tp) REVERT: A 190 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7851 (mtm-85) REVERT: A 216 GLU cc_start: 0.8608 (tp30) cc_final: 0.8385 (tp30) REVERT: A 309 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: A 495 LEU cc_start: 0.8669 (mm) cc_final: 0.8400 (mm) REVERT: B 125 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6122 (tp) REVERT: B 309 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6389 (tt0) REVERT: B 395 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.5739 (tp) REVERT: B 429 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6601 (p90) REVERT: B 466 MET cc_start: 0.8566 (mmm) cc_final: 0.8006 (mmm) REVERT: B 578 MET cc_start: 0.5727 (pmm) cc_final: 0.5382 (pmm) outliers start: 75 outliers final: 58 residues processed: 182 average time/residue: 0.1652 time to fit residues: 44.3020 Evaluate side-chains 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 42 THR 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 96 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 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 280 THR 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 318 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 371 THR 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 466 MET Chi-restraints excluded: chain A residue 481 LEU 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 35 ILE Chi-restraints excluded: chain B residue 40 SER 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 245 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 320 THR Chi-restraints excluded: chain B residue 362 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 102 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.205148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152675 restraints weight = 11395.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.152736 restraints weight = 11743.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155429 restraints weight = 9311.863| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9050 Z= 0.176 Angle : 0.613 11.414 12230 Z= 0.303 Chirality : 0.041 0.178 1454 Planarity : 0.004 0.038 1548 Dihedral : 3.896 22.556 1250 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.40 % Allowed : 24.44 % Favored : 71.17 % 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: 1.14 (0.25), residues: 1146 helix: 1.54 (0.19), residues: 756 sheet: 0.47 (0.81), residues: 44 loop : -0.94 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 66 HIS 0.006 0.001 HIS A 107 PHE 0.023 0.002 PHE A 429 TYR 0.022 0.001 TYR B 268 ARG 0.003 0.000 ARG A 190 *********************** 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 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.7959 (t70) cc_final: 0.7532 (t70) REVERT: A 190 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: A 242 MET cc_start: 0.7107 (mmt) cc_final: 0.6769 (mmt) REVERT: A 309 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6130 (tt0) REVERT: B 242 MET cc_start: 0.8004 (tpp) cc_final: 0.7724 (mmm) REVERT: B 395 ILE cc_start: 0.6378 (OUTLIER) cc_final: 0.5752 (tp) REVERT: B 429 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.6116 (p90) REVERT: B 466 MET cc_start: 0.8545 (mmm) cc_final: 0.7990 (mmm) outliers start: 43 outliers final: 35 residues processed: 166 average time/residue: 0.1960 time to fit residues: 46.8572 Evaluate side-chains 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 280 THR 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 362 ILE Chi-restraints excluded: chain A residue 371 THR 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 562 HIS Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 123 THR 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 245 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain B residue 272 PHE 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 429 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU 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 76 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 537 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.204423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151216 restraints weight = 11315.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149933 restraints weight = 11273.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153483 restraints weight = 8777.210| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9050 Z= 0.196 Angle : 0.634 15.141 12230 Z= 0.314 Chirality : 0.041 0.171 1454 Planarity : 0.004 0.038 1548 Dihedral : 3.891 22.396 1250 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.70 % Allowed : 24.34 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1146 helix: 1.57 (0.19), residues: 754 sheet: 0.59 (0.82), residues: 44 loop : -0.94 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 66 HIS 0.006 0.001 HIS A 107 PHE 0.020 0.002 PHE A 429 TYR 0.022 0.001 TYR B 268 ARG 0.009 0.000 ARG B 61 *********************** 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 177 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.8072 (t70) cc_final: 0.7682 (t70) REVERT: A 190 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7972 (mtm-85) REVERT: A 196 MET cc_start: 0.4850 (tpp) cc_final: 0.4323 (tpp) REVERT: A 309 GLN cc_start: 0.6604 (OUTLIER) cc_final: 0.6300 (tt0) REVERT: A 465 LYS cc_start: 0.8963 (tttt) cc_final: 0.8408 (pttp) REVERT: B 242 MET cc_start: 0.8043 (tpp) cc_final: 0.7738 (mmm) REVERT: B 309 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6289 (tt0) REVERT: B 395 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.5960 (tp) REVERT: B 429 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.6006 (p90) REVERT: B 466 MET cc_start: 0.8546 (mmm) cc_final: 0.7976 (mmm) outliers start: 46 outliers final: 37 residues processed: 164 average time/residue: 0.2012 time to fit residues: 46.5337 Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 280 THR 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 362 ILE Chi-restraints excluded: chain A residue 371 THR 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 577 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 123 THR 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 245 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 309 GLN 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 495 LEU Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 537 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 = 0.4397 r_free = 0.4397 target = 0.205365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.151730 restraints weight = 11395.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150582 restraints weight = 10960.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153383 restraints weight = 8875.087| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9050 Z= 0.190 Angle : 0.631 14.811 12230 Z= 0.312 Chirality : 0.041 0.169 1454 Planarity : 0.004 0.044 1548 Dihedral : 3.899 22.058 1250 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.81 % Allowed : 24.85 % Favored : 70.35 % 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: 1.14 (0.25), residues: 1146 helix: 1.55 (0.19), residues: 754 sheet: 2.49 (1.12), residues: 24 loop : -1.04 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 66 HIS 0.006 0.001 HIS A 107 PHE 0.022 0.002 PHE A 13 TYR 0.022 0.001 TYR B 268 ARG 0.005 0.000 ARG B 61 ********************** 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 174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 HIS cc_start: 0.8005 (t70) cc_final: 0.7591 (t70) REVERT: A 125 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6012 (tp) REVERT: A 309 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6323 (tt0) REVERT: A 465 LYS cc_start: 0.8962 (tttt) cc_final: 0.8419 (pttp) REVERT: B 113 VAL cc_start: 0.6532 (OUTLIER) cc_final: 0.5977 (t) REVERT: B 242 MET cc_start: 0.7973 (tpp) cc_final: 0.7715 (mmm) REVERT: B 309 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: B 429 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.6026 (p90) REVERT: B 466 MET cc_start: 0.8573 (mmm) cc_final: 0.8024 (mmm) outliers start: 47 outliers final: 41 residues processed: 163 average time/residue: 0.1873 time to fit residues: 44.7020 Evaluate side-chains 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 88 CYS Chi-restraints excluded: chain A residue 108 MET 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 245 VAL Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 280 THR 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 362 ILE Chi-restraints excluded: chain A residue 371 THR 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 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 113 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 173 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 245 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 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 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 495 LEU Chi-restraints excluded: chain B residue 502 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 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 537 HIS B 537 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.208554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154743 restraints weight = 11349.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.153583 restraints weight = 11789.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.156213 restraints weight = 8307.473| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9050 Z= 0.167 Angle : 0.614 15.319 12230 Z= 0.303 Chirality : 0.041 0.165 1454 Planarity : 0.004 0.045 1548 Dihedral : 3.847 21.415 1250 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.60 % Allowed : 24.85 % Favored : 70.55 % 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: 1.23 (0.25), residues: 1146 helix: 1.62 (0.19), residues: 756 sheet: 2.57 (1.12), residues: 24 loop : -1.02 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 66 HIS 0.006 0.001 HIS A 107 PHE 0.015 0.001 PHE B 116 TYR 0.021 0.001 TYR B 268 ARG 0.008 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2581.75 seconds wall clock time: 47 minutes 2.05 seconds (2822.05 seconds total)