Starting phenix.real_space_refine on Mon Nov 18 23:29:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttq_41612/11_2024/8ttq_41612.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttq_41612/11_2024/8ttq_41612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttq_41612/11_2024/8ttq_41612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttq_41612/11_2024/8ttq_41612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttq_41612/11_2024/8ttq_41612.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttq_41612/11_2024/8ttq_41612.cif" } resolution = 3.27 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= 0.002 sd= 0.033 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 5870 2.51 5 N 1620 2.21 5 O 1725 1.98 5 H 8353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17632 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 8806 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 28, 'TRANS': 575} Chain breaks: 9 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 7, 'GLU:plan': 8, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 8826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 8826 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 28, 'TRANS': 579} Chain breaks: 9 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 465 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 8, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 217 Time building chain proxies: 8.76, per 1000 atoms: 0.50 Number of scatterers: 17632 At special positions: 0 Unit cell: (132.825, 129.525, 91.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 O 1725 8.00 N 1620 7.00 C 5870 6.00 H 8353 1.00 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: 4.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2302 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 22 sheets defined 21.2% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 157 through 188 Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.799A pdb=" N GLN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 235 removed outlier: 4.326A pdb=" N GLU A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.624A pdb=" N ASP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 647 Processing helix chain 'A' and resid 704 through 716 removed outlier: 3.882A pdb=" N THR A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 157 through 188 Proline residue: B 163 - end of helix Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.832A pdb=" N SER B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.677A pdb=" N ILE B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 removed outlier: 4.019A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.674A pdb=" N ASN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 266' Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 627 through 646 removed outlier: 3.725A pdb=" N GLU B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 716 removed outlier: 3.651A pdb=" N GLN B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 711 " --> pdb=" O ARG B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.605A pdb=" N ILE A 155 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL A 68 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 12.064A pdb=" N LEU A 58 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 11.022A pdb=" N LEU A 136 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 12.053A pdb=" N LEU A 60 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.901A pdb=" N VAL A 134 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N LEU A 62 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 11.734A pdb=" N LYS A 132 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N ARG A 64 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE A 130 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N CYS A 128 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN A 94 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS A 86 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 138 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 84 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A 87 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 103 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 89 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N MET A 93 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 23 removed outlier: 6.913A pdb=" N ILE A 59 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 279 removed outlier: 5.879A pdb=" N ALA A 302 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N CYS A 312 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER A 304 " --> pdb=" O TRP A 310 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP A 310 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 330 through 334 removed outlier: 3.970A pdb=" N LYS A 330 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE A 361 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.588A pdb=" N PHE A 388 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 407 " --> pdb=" O PHE A 388 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 395 removed outlier: 3.607A pdb=" N THR A 403 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 428 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 441 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 457 through 464 removed outlier: 4.977A pdb=" N HIS A 459 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 474 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET A 461 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 472 " --> pdb=" O MET A 461 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 470 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 464 removed outlier: 4.977A pdb=" N HIS A 459 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 474 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET A 461 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 472 " --> pdb=" O MET A 461 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 470 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 517 through 521 Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AB4, first strand: chain 'B' and resid 14 through 16 removed outlier: 4.473A pdb=" N LEU B 152 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 149 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 155 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL B 68 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ARG B 129 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS B 86 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER B 138 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 84 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 89 " --> pdb=" O LEU B 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.788A pdb=" N ILE B 59 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 253 Processing sheet with id=AB8, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.500A pdb=" N VAL B 277 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE B 300 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 330 through 334 removed outlier: 6.408A pdb=" N ARG B 363 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU B 373 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP B 365 " --> pdb=" O TRP B 371 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TRP B 371 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.758A pdb=" N ARG B 407 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.710A pdb=" N THR B 403 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 430 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU B 440 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN B 432 " --> pdb=" O TRP B 438 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 438 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 459 through 464 removed outlier: 6.539A pdb=" N PHE B 485 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 516 through 521 removed outlier: 3.501A pdb=" N ILE B 527 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR B 551 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP B 552 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 557 " --> pdb=" O ASP B 552 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 912 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: 7.35 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8315 1.03 - 1.23: 38 1.23 - 1.42: 4142 1.42 - 1.61: 5271 1.61 - 1.81: 90 Bond restraints: 17856 Sorted by residual: bond pdb=" N CYS B 13 " pdb=" CA CYS B 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N CYS A 13 " pdb=" CA CYS A 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N CYS A 13 " pdb=" H CYS A 13 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" N CYS B 13 " pdb=" H CYS B 13 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" CB MET B 372 " pdb=" CG MET B 372 " ideal model delta sigma weight residual 1.520 1.537 -0.017 3.00e-02 1.11e+03 3.04e-01 ... (remaining 17851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 29849 0.94 - 1.88: 2005 1.88 - 2.82: 46 2.82 - 3.75: 43 3.75 - 4.69: 9 Bond angle restraints: 31952 Sorted by residual: angle pdb=" N ARG A 129 " pdb=" CA ARG A 129 " pdb=" C ARG A 129 " ideal model delta sigma weight residual 114.04 110.70 3.34 1.24e+00 6.50e-01 7.28e+00 angle pdb=" N LEU B 347 " pdb=" CA LEU B 347 " pdb=" C LEU B 347 " ideal model delta sigma weight residual 108.34 110.64 -2.30 1.31e+00 5.83e-01 3.07e+00 angle pdb=" N ILE B 202 " pdb=" CA ILE B 202 " pdb=" C ILE B 202 " ideal model delta sigma weight residual 109.34 112.77 -3.43 2.08e+00 2.31e-01 2.71e+00 angle pdb=" CA ILE B 202 " pdb=" C ILE B 202 " pdb=" N ALA B 203 " ideal model delta sigma weight residual 116.60 118.81 -2.21 1.45e+00 4.76e-01 2.32e+00 angle pdb=" CA CYS A 13 " pdb=" N CYS A 13 " pdb=" H CYS A 13 " ideal model delta sigma weight residual 114.00 109.50 4.50 3.00e+00 1.11e-01 2.25e+00 ... (remaining 31947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7903 17.47 - 34.94: 524 34.94 - 52.41: 131 52.41 - 69.88: 59 69.88 - 87.35: 8 Dihedral angle restraints: 8625 sinusoidal: 4366 harmonic: 4259 Sorted by residual: dihedral pdb=" CG ARG B 271 " pdb=" CD ARG B 271 " pdb=" NE ARG B 271 " pdb=" CZ ARG B 271 " ideal model delta sinusoidal sigma weight residual -90.00 -129.88 39.88 2 1.50e+01 4.44e-03 8.77e+00 dihedral pdb=" CB MET B 400 " pdb=" CG MET B 400 " pdb=" SD MET B 400 " pdb=" CE MET B 400 " ideal model delta sinusoidal sigma weight residual 60.00 108.28 -48.28 3 1.50e+01 4.44e-03 8.62e+00 dihedral pdb=" CA GLN B 476 " pdb=" CB GLN B 476 " pdb=" CG GLN B 476 " pdb=" CD GLN B 476 " ideal model delta sinusoidal sigma weight residual 60.00 108.23 -48.23 3 1.50e+01 4.44e-03 8.61e+00 ... (remaining 8622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 854 0.027 - 0.055: 375 0.055 - 0.082: 61 0.082 - 0.109: 66 0.109 - 0.136: 27 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CA ILE B 255 " pdb=" N ILE B 255 " pdb=" C ILE B 255 " pdb=" CB ILE B 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE B 133 " pdb=" N ILE B 133 " pdb=" C ILE B 133 " pdb=" CB ILE B 133 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1380 not shown) Planarity restraints: 2813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 31 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 32 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 162 " -0.015 5.00e-02 4.00e+02 2.21e-02 7.81e-01 pdb=" N PRO A 163 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 54 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.72e-01 pdb=" N PRO A 55 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " -0.013 5.00e-02 4.00e+02 ... (remaining 2810 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1621 2.22 - 2.82: 37453 2.82 - 3.41: 46299 3.41 - 4.01: 63395 4.01 - 4.60: 95632 Nonbonded interactions: 244400 Sorted by model distance: nonbonded pdb=" OD2 ASP B 334 " pdb=" H ARG B 337 " model vdw 1.631 2.450 nonbonded pdb=" OE1 GLU B 593 " pdb=" H GLU B 593 " model vdw 1.634 2.450 nonbonded pdb=" O THR B 515 " pdb=" H GLY B 532 " model vdw 1.670 2.450 nonbonded pdb="HE22 GLN B 339 " pdb=" OD1 ASP B 365 " model vdw 1.670 2.450 nonbonded pdb=" O PHE B 585 " pdb=" H ASN B 604 " model vdw 1.673 2.450 ... (remaining 244395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 202 or (resid 203 through 206 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 207 throug \ h 411 or resid 421 through 533 or resid 546 through 562 or resid 582 through 646 \ or resid 703 through 733)) selection = (chain 'B' and (resid 13 through 191 or (resid 192 through 206 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 207 throug \ h 217 or resid 222 through 257 or resid 265 through 594 or (resid 595 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 o \ r name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 \ or name HE1 or name HE2)) or resid 596 through 605 or resid 609 through 646 or r \ esid 703 through 733)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.320 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 39.820 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.002 0.033 9503 Z= 0.104 Angle : 0.403 4.693 12887 Z= 0.209 Chirality : 0.038 0.136 1383 Planarity : 0.002 0.026 1675 Dihedral : 13.160 77.747 3335 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.58 (0.25), residues: 1172 helix: 3.01 (0.38), residues: 212 sheet: 0.07 (0.31), residues: 302 loop : -0.30 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.002 0.000 HIS A 598 PHE 0.008 0.001 PHE A 184 TYR 0.009 0.001 TYR A 591 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.4243 time to fit residues: 37.6545 Evaluate side-chains 51 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 588 GLN B 187 HIS B 399 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9503 Z= 0.279 Angle : 0.478 5.347 12887 Z= 0.254 Chirality : 0.038 0.139 1383 Planarity : 0.003 0.026 1675 Dihedral : 3.242 15.710 1292 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.22 % Allowed : 2.69 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1172 helix: 3.63 (0.36), residues: 200 sheet: -0.41 (0.30), residues: 305 loop : -0.31 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 167 HIS 0.004 0.001 HIS A 598 PHE 0.013 0.001 PHE B 601 TYR 0.010 0.001 TYR A 591 ARG 0.003 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 53 average time/residue: 0.4523 time to fit residues: 35.7209 Evaluate side-chains 49 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9503 Z= 0.245 Angle : 0.456 5.329 12887 Z= 0.241 Chirality : 0.038 0.129 1383 Planarity : 0.003 0.026 1675 Dihedral : 3.331 16.438 1292 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.65 % Allowed : 3.12 % Favored : 96.23 % 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: 0.48 (0.25), residues: 1172 helix: 3.89 (0.35), residues: 201 sheet: -0.44 (0.30), residues: 303 loop : -0.41 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 371 HIS 0.003 0.001 HIS A 274 PHE 0.018 0.001 PHE B 618 TYR 0.009 0.001 TYR B 168 ARG 0.003 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8472 (mtp) cc_final: 0.8017 (mtp) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.4463 time to fit residues: 35.6021 Evaluate side-chains 50 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9503 Z= 0.331 Angle : 0.503 5.644 12887 Z= 0.269 Chirality : 0.038 0.136 1383 Planarity : 0.004 0.036 1675 Dihedral : 3.717 17.768 1292 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.54 % Allowed : 4.85 % Favored : 94.61 % 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: 0.21 (0.25), residues: 1172 helix: 3.69 (0.35), residues: 208 sheet: -0.64 (0.29), residues: 306 loop : -0.63 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 371 HIS 0.005 0.001 HIS A 274 PHE 0.017 0.002 PHE B 618 TYR 0.013 0.001 TYR B 286 ARG 0.003 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8415 (mtp) cc_final: 0.8009 (mtp) REVERT: A 184 PHE cc_start: 0.8891 (m-80) cc_final: 0.8490 (m-10) REVERT: A 400 MET cc_start: 0.8203 (tpp) cc_final: 0.7925 (tpp) REVERT: B 400 MET cc_start: 0.8588 (mmp) cc_final: 0.7661 (mmm) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.4042 time to fit residues: 30.6458 Evaluate side-chains 47 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain B residue 387 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 9503 Z= 0.257 Angle : 0.471 6.456 12887 Z= 0.248 Chirality : 0.038 0.133 1383 Planarity : 0.003 0.031 1675 Dihedral : 3.623 16.428 1292 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.75 % Allowed : 5.17 % Favored : 94.07 % 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 (0.25), residues: 1172 helix: 4.09 (0.35), residues: 201 sheet: -0.69 (0.29), residues: 302 loop : -0.57 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 371 HIS 0.004 0.001 HIS A 274 PHE 0.011 0.001 PHE A 485 TYR 0.011 0.001 TYR B 168 ARG 0.003 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8386 (mtp) cc_final: 0.7989 (mtp) REVERT: A 184 PHE cc_start: 0.8907 (m-80) cc_final: 0.8476 (m-10) REVERT: A 461 MET cc_start: 0.8827 (ttp) cc_final: 0.8550 (ttp) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.4260 time to fit residues: 32.9724 Evaluate side-chains 49 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 551 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9503 Z= 0.290 Angle : 0.482 5.589 12887 Z= 0.257 Chirality : 0.038 0.130 1383 Planarity : 0.004 0.042 1675 Dihedral : 3.737 16.726 1292 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.08 % Allowed : 6.25 % Favored : 92.67 % 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: 0.16 (0.25), residues: 1172 helix: 3.81 (0.35), residues: 208 sheet: -0.76 (0.30), residues: 298 loop : -0.69 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 371 HIS 0.005 0.001 HIS A 274 PHE 0.019 0.001 PHE B 618 TYR 0.013 0.001 TYR B 168 ARG 0.004 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8369 (mtp) cc_final: 0.7990 (mtp) REVERT: B 184 PHE cc_start: 0.8456 (m-10) cc_final: 0.8216 (m-10) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.4118 time to fit residues: 33.0254 Evaluate side-chains 52 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 551 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9503 Z= 0.204 Angle : 0.449 5.480 12887 Z= 0.236 Chirality : 0.038 0.134 1383 Planarity : 0.003 0.037 1675 Dihedral : 3.610 17.004 1292 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.08 % Allowed : 7.00 % Favored : 91.92 % 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: 0.24 (0.25), residues: 1172 helix: 4.02 (0.35), residues: 208 sheet: -0.82 (0.30), residues: 293 loop : -0.63 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 139 HIS 0.004 0.001 HIS A 274 PHE 0.009 0.001 PHE B 618 TYR 0.010 0.001 TYR B 168 ARG 0.004 0.000 ARG A 614 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8375 (mtp) cc_final: 0.7999 (mtp) REVERT: A 184 PHE cc_start: 0.8951 (m-80) cc_final: 0.8495 (m-10) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.4091 time to fit residues: 33.1191 Evaluate side-chains 49 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 551 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9503 Z= 0.210 Angle : 0.455 5.472 12887 Z= 0.238 Chirality : 0.038 0.136 1383 Planarity : 0.003 0.031 1675 Dihedral : 3.581 17.007 1292 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.08 % Allowed : 7.54 % Favored : 91.38 % 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: 0.27 (0.26), residues: 1172 helix: 4.09 (0.35), residues: 208 sheet: -0.77 (0.30), residues: 292 loop : -0.64 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 139 HIS 0.003 0.001 HIS A 274 PHE 0.022 0.001 PHE B 184 TYR 0.011 0.001 TYR B 168 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8357 (mtp) cc_final: 0.7975 (mtp) REVERT: A 184 PHE cc_start: 0.8946 (m-80) cc_final: 0.8491 (m-10) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.4053 time to fit residues: 32.9180 Evaluate side-chains 51 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 551 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 0.0870 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9503 Z= 0.193 Angle : 0.450 6.409 12887 Z= 0.234 Chirality : 0.038 0.135 1383 Planarity : 0.003 0.030 1675 Dihedral : 3.543 16.952 1292 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.97 % Allowed : 7.65 % Favored : 91.38 % 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 (0.26), residues: 1172 helix: 4.18 (0.35), residues: 208 sheet: -0.76 (0.30), residues: 291 loop : -0.64 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 139 HIS 0.002 0.001 HIS A 598 PHE 0.015 0.001 PHE B 184 TYR 0.011 0.001 TYR B 168 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8363 (mtp) cc_final: 0.7974 (mtp) REVERT: A 184 PHE cc_start: 0.8944 (m-80) cc_final: 0.8486 (m-10) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.4154 time to fit residues: 32.1536 Evaluate side-chains 50 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 551 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 0.0970 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9503 Z= 0.193 Angle : 0.448 5.461 12887 Z= 0.233 Chirality : 0.038 0.132 1383 Planarity : 0.003 0.030 1675 Dihedral : 3.536 16.899 1292 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.97 % Allowed : 7.65 % Favored : 91.38 % 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 (0.26), residues: 1172 helix: 4.23 (0.35), residues: 208 sheet: -0.79 (0.30), residues: 293 loop : -0.63 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 139 HIS 0.006 0.001 HIS A 598 PHE 0.013 0.001 PHE B 184 TYR 0.011 0.001 TYR B 168 ARG 0.002 0.000 ARG A 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue ALA 192 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 647 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue SER 195 is missing expected H atoms. Skipping. Residue LEU 196 is missing expected H atoms. Skipping. Residue LYS 198 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 201 is missing expected H atoms. Skipping. Residue ILE 202 is missing expected H atoms. Skipping. Residue ALA 203 is missing expected H atoms. Skipping. Residue LEU 204 is missing expected H atoms. Skipping. Residue MET 208 is missing expected H atoms. Skipping. Residue LEU 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue ILE 212 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue ALA 224 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LYS 231 is missing expected H atoms. Skipping. Residue ALA 232 is missing expected H atoms. Skipping. Residue VAL 233 is missing expected H atoms. Skipping. Residue LEU 237 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue ILE 242 is missing expected H atoms. Skipping. Residue SER 243 is missing expected H atoms. Skipping. Residue SER 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue TYR 630 is missing expected H atoms. Skipping. Residue LEU 631 is missing expected H atoms. Skipping. Residue LEU 632 is missing expected H atoms. Skipping. Residue LYS 636 is missing expected H atoms. Skipping. Residue TYR 637 is missing expected H atoms. Skipping. Residue LEU 638 is missing expected H atoms. Skipping. Residue ILE 639 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue THR 703 is missing expected H atoms. Skipping. Residue TYR 704 is missing expected H atoms. Skipping. Residue ALA 705 is missing expected H atoms. Skipping. Residue THR 708 is missing expected H atoms. Skipping. Residue LEU 710 is missing expected H atoms. Skipping. Residue THR 713 is missing expected H atoms. Skipping. Residue LEU 714 is missing expected H atoms. Skipping. Residue VAL 715 is missing expected H atoms. Skipping. Residue SER 721 is missing expected H atoms. Skipping. Residue MET 722 is missing expected H atoms. Skipping. Residue THR 723 is missing expected H atoms. Skipping. Residue LYS 726 is missing expected H atoms. Skipping. Residue LEU 729 is missing expected H atoms. Skipping. Residue VAL 730 is missing expected H atoms. Skipping. Residue LEU 732 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8937 (m-80) cc_final: 0.8482 (m-10) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.4137 time to fit residues: 32.2775 Evaluate side-chains 50 residues out of total 1117 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 TRP Chi-restraints excluded: chain A residue 582 CYS Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 551 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.060982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.050044 restraints weight = 142922.630| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.34 r_work: 0.3143 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9503 Z= 0.216 Angle : 0.462 8.698 12887 Z= 0.240 Chirality : 0.038 0.134 1383 Planarity : 0.003 0.030 1675 Dihedral : 3.591 16.827 1292 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.97 % Allowed : 7.54 % Favored : 91.49 % 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: 0.28 (0.26), residues: 1172 helix: 4.25 (0.35), residues: 208 sheet: -0.84 (0.30), residues: 293 loop : -0.66 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 251 HIS 0.003 0.001 HIS A 598 PHE 0.016 0.001 PHE B 618 TYR 0.013 0.001 TYR A 591 ARG 0.003 0.000 ARG A 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.10 seconds wall clock time: 67 minutes 0.04 seconds (4020.04 seconds total)