Starting phenix.real_space_refine on Fri Mar 15 10:56:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9z_21132/03_2024/6v9z_21132.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9z_21132/03_2024/6v9z_21132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9z_21132/03_2024/6v9z_21132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9z_21132/03_2024/6v9z_21132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9z_21132/03_2024/6v9z_21132.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9z_21132/03_2024/6v9z_21132.pdb" } resolution = 3.35 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 7386 2.51 5 N 1868 2.21 5 O 2122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 468": "OE1" <-> "OE2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 625": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11434 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5580 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 147 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5580 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 127 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.37, per 1000 atoms: 0.56 Number of scatterers: 11434 At special positions: 0 Unit cell: (104.64, 105.73, 139.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2122 8.00 N 1868 7.00 C 7386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 2.3 seconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 64.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.501A pdb=" N LYS A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.751A pdb=" N VAL A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 203 through 252 removed outlier: 3.602A pdb=" N ALA A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.949A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 305 removed outlier: 4.428A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 354 removed outlier: 4.641A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.592A pdb=" N GLY A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.680A pdb=" N GLU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.799A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.843A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 445 through 464 removed outlier: 4.208A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.555A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.550A pdb=" N CYS A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 removed outlier: 3.515A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 598 " --> pdb=" O LYS A 594 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 624 through 640 removed outlier: 3.814A pdb=" N ARG A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 removed outlier: 4.150A pdb=" N HIS A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 685 removed outlier: 4.337A pdb=" N ILE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.642A pdb=" N LYS A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'B' and resid 21 through 34 Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.503A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 165 through 187 removed outlier: 3.788A pdb=" N VAL B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 203 through 252 removed outlier: 3.599A pdb=" N ALA B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.955A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 305 removed outlier: 4.566A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 removed outlier: 4.654A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.611A pdb=" N GLY B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 417 removed outlier: 3.707A pdb=" N GLU B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 removed outlier: 3.819A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.805A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 445 through 464 removed outlier: 4.227A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 521 through 533 removed outlier: 3.560A pdb=" N ALA B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 575 through 581 removed outlier: 3.633A pdb=" N CYS B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 600 removed outlier: 3.515A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 624 through 640 removed outlier: 3.533A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 4.165A pdb=" N HIS B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 685 removed outlier: 4.343A pdb=" N ILE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.639A pdb=" N LYS B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 73 removed outlier: 4.297A pdb=" N GLY A 135 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.598A pdb=" N PHE A 488 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.589A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N TYR A 691 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 516 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 693 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 518 " --> pdb=" O LEU A 693 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.664A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY B 135 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE B 92 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 133 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D 11 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 506 through 509 removed outlier: 3.572A pdb=" N PHE B 488 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 562 through 565 removed outlier: 6.560A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) 711 hydrogen bonds defined for protein. 2058 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: 3.82 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2319 1.34 - 1.46: 2394 1.46 - 1.58: 6793 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 11608 Sorted by residual: bond pdb=" N LYS A 328 " pdb=" CA LYS A 328 " ideal model delta sigma weight residual 1.463 1.493 -0.030 6.90e-03 2.10e+04 1.89e+01 bond pdb=" N LYS B 328 " pdb=" CA LYS B 328 " ideal model delta sigma weight residual 1.463 1.492 -0.029 6.90e-03 2.10e+04 1.78e+01 bond pdb=" N LYS B 163 " pdb=" CA LYS B 163 " ideal model delta sigma weight residual 1.462 1.493 -0.031 8.50e-03 1.38e+04 1.32e+01 bond pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 1.461 1.504 -0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" N ILE B 289 " pdb=" CA ILE B 289 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.09e-02 8.42e+03 1.31e+01 ... (remaining 11603 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.92: 184 106.92 - 113.77: 6351 113.77 - 120.62: 5170 120.62 - 127.46: 3904 127.46 - 134.31: 37 Bond angle restraints: 15646 Sorted by residual: angle pdb=" N ILE A 276 " pdb=" CA ILE A 276 " pdb=" CB ILE A 276 " ideal model delta sigma weight residual 110.55 116.75 -6.20 1.17e+00 7.31e-01 2.81e+01 angle pdb=" C ALA B 159 " pdb=" N GLY B 160 " pdb=" CA GLY B 160 " ideal model delta sigma weight residual 120.03 125.68 -5.65 1.12e+00 7.97e-01 2.55e+01 angle pdb=" C ALA A 159 " pdb=" N GLY A 160 " pdb=" CA GLY A 160 " ideal model delta sigma weight residual 120.03 125.63 -5.60 1.12e+00 7.97e-01 2.50e+01 angle pdb=" C GLU A 625 " pdb=" N GLY A 626 " pdb=" CA GLY A 626 " ideal model delta sigma weight residual 120.03 125.51 -5.48 1.12e+00 7.97e-01 2.39e+01 angle pdb=" C GLY B 297 " pdb=" N GLY B 298 " pdb=" CA GLY B 298 " ideal model delta sigma weight residual 119.94 125.37 -5.43 1.11e+00 8.12e-01 2.39e+01 ... (remaining 15641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 6301 17.01 - 34.02: 539 34.02 - 51.04: 145 51.04 - 68.05: 31 68.05 - 85.06: 6 Dihedral angle restraints: 7022 sinusoidal: 2776 harmonic: 4246 Sorted by residual: dihedral pdb=" CA LEU A 85 " pdb=" C LEU A 85 " pdb=" N PRO A 86 " pdb=" CA PRO A 86 " ideal model delta harmonic sigma weight residual 0.00 28.41 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP A 132 " pdb=" C TRP A 132 " pdb=" N THR A 133 " pdb=" CA THR A 133 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA TRP B 132 " pdb=" C TRP B 132 " pdb=" N THR B 133 " pdb=" CA THR B 133 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 7019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 629 0.048 - 0.096: 685 0.096 - 0.144: 406 0.144 - 0.192: 119 0.192 - 0.240: 13 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE B 486 " pdb=" N ILE B 486 " pdb=" C ILE B 486 " pdb=" CB ILE B 486 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE A 486 " pdb=" N ILE A 486 " pdb=" C ILE A 486 " pdb=" CB ILE A 486 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1849 not shown) Planarity restraints: 1950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 611 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C LYS A 611 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS A 611 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR A 612 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 94 " 0.006 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C ASP B 94 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP B 94 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 132 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C TRP B 132 " -0.022 2.00e-02 2.50e+03 pdb=" O TRP B 132 " 0.008 2.00e-02 2.50e+03 pdb=" N THR B 133 " 0.008 2.00e-02 2.50e+03 ... (remaining 1947 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2545 2.89 - 3.39: 12424 3.39 - 3.89: 18251 3.89 - 4.40: 19316 4.40 - 4.90: 34882 Nonbonded interactions: 87418 Sorted by model distance: nonbonded pdb=" O VAL A 11 " pdb=" OH TYR A 104 " model vdw 2.382 2.440 nonbonded pdb=" O VAL B 11 " pdb=" OH TYR B 104 " model vdw 2.393 2.440 nonbonded pdb=" O ALA A 98 " pdb=" CA GLY C 24 " model vdw 2.431 3.440 nonbonded pdb=" O LEU A 610 " pdb=" OG1 THR A 614 " model vdw 2.432 2.440 nonbonded pdb=" O LEU B 610 " pdb=" OG1 THR B 614 " model vdw 2.486 2.440 ... (remaining 87413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.240 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 32.730 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.014 0.045 11608 Z= 0.910 Angle : 1.878 7.751 15646 Z= 1.442 Chirality : 0.086 0.240 1852 Planarity : 0.003 0.019 1950 Dihedral : 14.269 85.061 4294 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.97 % Allowed : 9.73 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.85 (0.18), residues: 1464 helix: -1.56 (0.14), residues: 864 sheet: -2.13 (0.41), residues: 118 loop : -2.12 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 132 HIS 0.006 0.002 HIS B 660 PHE 0.020 0.002 PHE B 67 TYR 0.018 0.002 TYR A 246 ARG 0.006 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8726 (ttm) cc_final: 0.8489 (ttt) REVERT: A 255 MET cc_start: 0.8441 (mmm) cc_final: 0.7880 (mmm) REVERT: A 278 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8308 (tm-30) REVERT: A 288 MET cc_start: 0.8212 (mtp) cc_final: 0.7928 (mmp) REVERT: A 340 ASP cc_start: 0.8631 (m-30) cc_final: 0.8326 (m-30) REVERT: A 478 PHE cc_start: 0.8052 (m-80) cc_final: 0.7816 (m-80) REVERT: A 567 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6139 (tp40) REVERT: A 647 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7814 (t70) REVERT: C 18 LEU cc_start: 0.8776 (mt) cc_final: 0.8542 (mm) REVERT: C 19 MET cc_start: 0.8493 (ttm) cc_final: 0.8274 (tpp) REVERT: C 20 GLU cc_start: 0.8751 (tt0) cc_final: 0.8493 (tp30) REVERT: B 81 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8337 (ttpp) REVERT: B 154 MET cc_start: 0.8266 (mmm) cc_final: 0.7855 (mmt) REVERT: B 243 MET cc_start: 0.8702 (mtm) cc_final: 0.8442 (mtt) REVERT: B 290 ASP cc_start: 0.8950 (m-30) cc_final: 0.8673 (m-30) REVERT: B 420 MET cc_start: 0.8959 (ptp) cc_final: 0.8570 (ptm) REVERT: B 517 ILE cc_start: 0.9207 (mt) cc_final: 0.8988 (mm) REVERT: B 589 MET cc_start: 0.8039 (tmm) cc_final: 0.7739 (tmm) REVERT: B 647 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8243 (t0) outliers start: 37 outliers final: 16 residues processed: 167 average time/residue: 0.2259 time to fit residues: 54.6151 Evaluate side-chains 102 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 259 ASN A 278 GLN A 629 GLN A 704 HIS B 99 HIS B 259 ASN B 278 GLN B 567 GLN B 617 ASN B 704 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11608 Z= 0.177 Angle : 0.521 8.004 15646 Z= 0.281 Chirality : 0.038 0.149 1852 Planarity : 0.003 0.020 1950 Dihedral : 6.177 55.826 1600 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.17 % Allowed : 13.99 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1464 helix: 1.81 (0.17), residues: 866 sheet: -1.01 (0.41), residues: 148 loop : -1.52 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 132 HIS 0.002 0.001 HIS A 602 PHE 0.014 0.001 PHE B 488 TYR 0.011 0.001 TYR A 225 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7516 (pp) REVERT: A 278 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: A 288 MET cc_start: 0.8424 (mtp) cc_final: 0.8033 (mmp) REVERT: A 420 MET cc_start: 0.9215 (ptm) cc_final: 0.8883 (ptm) REVERT: A 589 MET cc_start: 0.7601 (mmm) cc_final: 0.7267 (mmm) REVERT: A 647 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.7978 (t0) REVERT: B 420 MET cc_start: 0.8884 (ptp) cc_final: 0.8451 (ptm) REVERT: B 517 ILE cc_start: 0.9207 (mt) cc_final: 0.8974 (mm) REVERT: B 567 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: B 647 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8214 (t0) REVERT: D 20 GLU cc_start: 0.8914 (tp30) cc_final: 0.8603 (tm-30) outliers start: 27 outliers final: 15 residues processed: 108 average time/residue: 0.1990 time to fit residues: 33.1767 Evaluate side-chains 94 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11608 Z= 0.173 Angle : 0.470 6.564 15646 Z= 0.254 Chirality : 0.038 0.157 1852 Planarity : 0.002 0.026 1950 Dihedral : 5.276 58.572 1586 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.57 % Allowed : 15.19 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1464 helix: 2.59 (0.18), residues: 860 sheet: -0.56 (0.42), residues: 144 loop : -1.08 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS B 99 PHE 0.012 0.001 PHE B 257 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8625 (tpt) cc_final: 0.7883 (tmm) REVERT: A 271 MET cc_start: 0.8333 (tpp) cc_final: 0.8032 (tpp) REVERT: A 278 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: A 288 MET cc_start: 0.8414 (mtp) cc_final: 0.8040 (mmp) REVERT: A 338 MET cc_start: 0.8423 (mmm) cc_final: 0.8185 (mmt) REVERT: A 420 MET cc_start: 0.9247 (ptm) cc_final: 0.8967 (ptm) REVERT: B 125 MET cc_start: 0.7963 (tpp) cc_final: 0.6968 (tmm) REVERT: B 420 MET cc_start: 0.8703 (ptp) cc_final: 0.8317 (ptm) REVERT: B 517 ILE cc_start: 0.9179 (mt) cc_final: 0.8973 (mm) REVERT: B 647 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8409 (t0) REVERT: D 20 GLU cc_start: 0.8992 (tp30) cc_final: 0.8613 (tm-30) outliers start: 32 outliers final: 12 residues processed: 102 average time/residue: 0.1910 time to fit residues: 30.9526 Evaluate side-chains 82 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 567 GLN Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 647 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 14 optimal weight: 0.0000 chunk 62 optimal weight: 7.9990 chunk 88 optimal weight: 0.0270 chunk 132 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 overall best weight: 0.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11608 Z= 0.114 Angle : 0.441 7.456 15646 Z= 0.234 Chirality : 0.038 0.144 1852 Planarity : 0.002 0.017 1950 Dihedral : 4.594 59.097 1575 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.37 % Allowed : 16.16 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.08 (0.23), residues: 1464 helix: 2.81 (0.18), residues: 866 sheet: -0.38 (0.42), residues: 146 loop : -0.95 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.004 0.001 HIS B 602 PHE 0.011 0.001 PHE B 257 TYR 0.009 0.001 TYR A 225 ARG 0.001 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8586 (tpt) cc_final: 0.7744 (tmm) REVERT: A 271 MET cc_start: 0.8300 (tpp) cc_final: 0.7950 (tpp) REVERT: A 288 MET cc_start: 0.8460 (mtp) cc_final: 0.8059 (mmp) REVERT: A 420 MET cc_start: 0.9242 (ptm) cc_final: 0.9019 (ptm) REVERT: A 589 MET cc_start: 0.7237 (mmm) cc_final: 0.6851 (tmm) REVERT: A 598 MET cc_start: 0.9003 (mpp) cc_final: 0.8767 (mpp) REVERT: B 420 MET cc_start: 0.8716 (ptp) cc_final: 0.8311 (ptm) REVERT: D 17 GLU cc_start: 0.9193 (tp30) cc_final: 0.8958 (tp30) REVERT: D 20 GLU cc_start: 0.8914 (tp30) cc_final: 0.8477 (tm-30) outliers start: 17 outliers final: 8 residues processed: 98 average time/residue: 0.1831 time to fit residues: 29.0679 Evaluate side-chains 79 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 570 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11608 Z= 0.308 Angle : 0.542 7.711 15646 Z= 0.286 Chirality : 0.039 0.139 1852 Planarity : 0.002 0.018 1950 Dihedral : 4.237 59.566 1563 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 16.96 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.00 (0.23), residues: 1464 helix: 2.56 (0.18), residues: 876 sheet: -0.11 (0.43), residues: 142 loop : -0.76 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 718 HIS 0.005 0.001 HIS B 249 PHE 0.015 0.002 PHE B 257 TYR 0.012 0.001 TYR A 319 ARG 0.003 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8762 (tpt) cc_final: 0.7900 (tmm) REVERT: A 255 MET cc_start: 0.8295 (mmm) cc_final: 0.7689 (mmm) REVERT: A 271 MET cc_start: 0.8395 (tpp) cc_final: 0.8041 (tmm) REVERT: A 278 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: A 288 MET cc_start: 0.8599 (mtp) cc_final: 0.8217 (mmp) REVERT: A 338 MET cc_start: 0.8415 (mmm) cc_final: 0.8214 (mmt) REVERT: A 598 MET cc_start: 0.9063 (mpp) cc_final: 0.8630 (mpp) REVERT: C 17 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8699 (pm20) REVERT: B 125 MET cc_start: 0.8070 (tpp) cc_final: 0.7131 (tmm) REVERT: B 387 MET cc_start: 0.9102 (tpp) cc_final: 0.8879 (mpp) REVERT: B 420 MET cc_start: 0.8662 (ptp) cc_final: 0.8428 (ptm) REVERT: B 668 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9292 (mm) REVERT: D 20 GLU cc_start: 0.8978 (tp30) cc_final: 0.8652 (tm-30) outliers start: 24 outliers final: 12 residues processed: 91 average time/residue: 0.2081 time to fit residues: 30.6109 Evaluate side-chains 80 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11608 Z= 0.310 Angle : 0.539 8.296 15646 Z= 0.281 Chirality : 0.039 0.138 1852 Planarity : 0.002 0.017 1950 Dihedral : 4.199 58.678 1561 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.25 % Allowed : 17.04 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1464 helix: 2.47 (0.18), residues: 876 sheet: 0.07 (0.44), residues: 140 loop : -0.76 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 409 HIS 0.005 0.001 HIS B 249 PHE 0.017 0.001 PHE B 257 TYR 0.011 0.001 TYR A 225 ARG 0.002 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8811 (tpt) cc_final: 0.8007 (tmm) REVERT: A 255 MET cc_start: 0.8277 (mmm) cc_final: 0.7559 (mmm) REVERT: A 278 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 288 MET cc_start: 0.8633 (mtp) cc_final: 0.8249 (mmp) REVERT: A 387 MET cc_start: 0.9136 (tpp) cc_final: 0.8793 (tpp) REVERT: A 570 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6242 (t80) REVERT: A 598 MET cc_start: 0.9127 (mpp) cc_final: 0.8644 (mpp) REVERT: C 17 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: B 125 MET cc_start: 0.8010 (tpp) cc_final: 0.7145 (tmm) REVERT: B 387 MET cc_start: 0.9191 (tpp) cc_final: 0.8909 (mpp) REVERT: B 420 MET cc_start: 0.8682 (ptp) cc_final: 0.8319 (ptm) REVERT: B 668 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9296 (mm) REVERT: D 15 ASP cc_start: 0.8180 (t70) cc_final: 0.7740 (t70) REVERT: D 20 GLU cc_start: 0.8982 (tp30) cc_final: 0.8706 (tm-30) outliers start: 28 outliers final: 15 residues processed: 94 average time/residue: 0.1842 time to fit residues: 28.2239 Evaluate side-chains 85 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 139 optimal weight: 0.0470 chunk 87 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11608 Z= 0.128 Angle : 0.468 8.452 15646 Z= 0.241 Chirality : 0.038 0.147 1852 Planarity : 0.002 0.014 1950 Dihedral : 3.954 58.884 1561 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.77 % Allowed : 17.52 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.17 (0.23), residues: 1464 helix: 2.75 (0.18), residues: 866 sheet: -0.11 (0.42), residues: 164 loop : -0.70 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.003 0.000 HIS B 249 PHE 0.021 0.001 PHE A 128 TYR 0.011 0.001 TYR B 179 ARG 0.001 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8778 (tpt) cc_final: 0.7979 (tmm) REVERT: A 288 MET cc_start: 0.8650 (mtp) cc_final: 0.8180 (mmm) REVERT: A 338 MET cc_start: 0.8447 (mmm) cc_final: 0.8136 (mmt) REVERT: A 387 MET cc_start: 0.9026 (tpp) cc_final: 0.8641 (tpp) REVERT: A 570 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.6165 (t80) REVERT: A 589 MET cc_start: 0.7290 (mmm) cc_final: 0.7034 (mmm) REVERT: A 598 MET cc_start: 0.9029 (mpp) cc_final: 0.8650 (mpp) REVERT: C 17 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8746 (pm20) REVERT: B 125 MET cc_start: 0.8014 (tpp) cc_final: 0.7111 (tmm) REVERT: B 387 MET cc_start: 0.9105 (tpp) cc_final: 0.8863 (tpp) REVERT: B 420 MET cc_start: 0.8740 (ptp) cc_final: 0.8381 (ptm) REVERT: B 567 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7599 (mm-40) REVERT: B 668 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9308 (mm) REVERT: D 15 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7735 (t70) REVERT: D 20 GLU cc_start: 0.8931 (tp30) cc_final: 0.8568 (tm-30) outliers start: 22 outliers final: 8 residues processed: 93 average time/residue: 0.1883 time to fit residues: 28.2627 Evaluate side-chains 83 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain D residue 15 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 133 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11608 Z= 0.142 Angle : 0.465 11.143 15646 Z= 0.239 Chirality : 0.038 0.141 1852 Planarity : 0.002 0.012 1950 Dihedral : 3.896 59.059 1561 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.09 % Allowed : 17.44 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.23 (0.23), residues: 1464 helix: 2.77 (0.18), residues: 866 sheet: 0.07 (0.42), residues: 160 loop : -0.67 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.015 0.001 PHE A 428 TYR 0.010 0.001 TYR A 225 ARG 0.001 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 72 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8723 (tpt) cc_final: 0.7937 (tmm) REVERT: A 271 MET cc_start: 0.8286 (tpp) cc_final: 0.7914 (tmm) REVERT: A 278 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: A 288 MET cc_start: 0.8650 (mtp) cc_final: 0.8161 (mmm) REVERT: A 338 MET cc_start: 0.8491 (mmm) cc_final: 0.8179 (mmt) REVERT: A 387 MET cc_start: 0.9022 (tpp) cc_final: 0.8653 (tpp) REVERT: A 570 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.6130 (t80) REVERT: A 589 MET cc_start: 0.7246 (mmm) cc_final: 0.6990 (mmm) REVERT: A 598 MET cc_start: 0.9028 (mpp) cc_final: 0.8660 (mpp) REVERT: A 648 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.5925 (tm-30) REVERT: B 125 MET cc_start: 0.8046 (tpp) cc_final: 0.7131 (tmm) REVERT: B 387 MET cc_start: 0.9089 (tpp) cc_final: 0.8841 (tpp) REVERT: B 420 MET cc_start: 0.8748 (ptp) cc_final: 0.8385 (ptm) REVERT: B 668 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9312 (mm) REVERT: D 15 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7740 (t70) REVERT: D 20 GLU cc_start: 0.8984 (tp30) cc_final: 0.8639 (tm-30) outliers start: 26 outliers final: 10 residues processed: 94 average time/residue: 0.1956 time to fit residues: 29.9865 Evaluate side-chains 83 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain D residue 15 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 133 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 117 optimal weight: 0.4980 chunk 123 optimal weight: 0.0670 chunk 129 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11608 Z= 0.121 Angle : 0.459 10.556 15646 Z= 0.233 Chirality : 0.038 0.142 1852 Planarity : 0.002 0.012 1950 Dihedral : 3.787 58.150 1561 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.61 % Allowed : 18.09 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.33 (0.23), residues: 1464 helix: 2.82 (0.18), residues: 870 sheet: 0.14 (0.42), residues: 160 loop : -0.63 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.002 0.000 HIS B 249 PHE 0.026 0.001 PHE A 128 TYR 0.010 0.001 TYR B 179 ARG 0.001 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8719 (tpt) cc_final: 0.7919 (tmm) REVERT: A 271 MET cc_start: 0.8283 (tpp) cc_final: 0.7918 (tmm) REVERT: A 278 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: A 288 MET cc_start: 0.8644 (mtp) cc_final: 0.8159 (mmm) REVERT: A 338 MET cc_start: 0.8512 (mmm) cc_final: 0.8212 (mmt) REVERT: A 387 MET cc_start: 0.9003 (tpp) cc_final: 0.8632 (tpp) REVERT: A 570 PHE cc_start: 0.6580 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 589 MET cc_start: 0.7260 (mmm) cc_final: 0.6990 (mmm) REVERT: A 598 MET cc_start: 0.9005 (mpp) cc_final: 0.8665 (mpp) REVERT: A 648 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.5888 (tm-30) REVERT: B 125 MET cc_start: 0.8051 (tpp) cc_final: 0.7128 (tmm) REVERT: B 255 MET cc_start: 0.8340 (mmm) cc_final: 0.7983 (mmm) REVERT: B 387 MET cc_start: 0.9054 (tpp) cc_final: 0.8854 (tpp) REVERT: B 668 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9299 (mm) REVERT: D 15 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7792 (t70) REVERT: D 20 GLU cc_start: 0.8982 (tp30) cc_final: 0.8772 (tm-30) outliers start: 20 outliers final: 8 residues processed: 90 average time/residue: 0.1845 time to fit residues: 26.8039 Evaluate side-chains 82 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain D residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11608 Z= 0.220 Angle : 0.509 11.118 15646 Z= 0.257 Chirality : 0.039 0.201 1852 Planarity : 0.002 0.012 1950 Dihedral : 3.864 56.105 1561 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.45 % Allowed : 18.09 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.31 (0.23), residues: 1464 helix: 2.78 (0.18), residues: 866 sheet: 0.17 (0.43), residues: 160 loop : -0.56 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 132 HIS 0.004 0.001 HIS B 249 PHE 0.015 0.001 PHE B 257 TYR 0.011 0.001 TYR A 225 ARG 0.002 0.000 ARG B 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8758 (tpt) cc_final: 0.7951 (tmm) REVERT: A 278 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: A 338 MET cc_start: 0.8537 (mmm) cc_final: 0.8246 (mmt) REVERT: A 387 MET cc_start: 0.9018 (tpp) cc_final: 0.8659 (tpp) REVERT: A 570 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.5796 (t80) REVERT: A 598 MET cc_start: 0.9076 (mpp) cc_final: 0.8692 (mpp) REVERT: A 648 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6057 (tm-30) REVERT: B 387 MET cc_start: 0.9106 (tpp) cc_final: 0.8854 (tpp) REVERT: B 668 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9286 (mm) REVERT: D 15 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7885 (t70) outliers start: 18 outliers final: 10 residues processed: 85 average time/residue: 0.1850 time to fit residues: 25.6728 Evaluate side-chains 83 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain D residue 15 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.067393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.056355 restraints weight = 46102.931| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.36 r_work: 0.3088 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 11608 Z= 0.144 Angle : 0.492 10.588 15646 Z= 0.247 Chirality : 0.038 0.196 1852 Planarity : 0.002 0.022 1950 Dihedral : 3.773 52.747 1561 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.21 % Allowed : 18.57 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.32 (0.23), residues: 1464 helix: 2.78 (0.18), residues: 870 sheet: 0.22 (0.43), residues: 160 loop : -0.58 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.003 0.001 HIS B 249 PHE 0.028 0.001 PHE A 128 TYR 0.010 0.001 TYR A 179 ARG 0.001 0.000 ARG A 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.07 seconds wall clock time: 38 minutes 47.39 seconds (2327.39 seconds total)