Starting phenix.real_space_refine on Tue Feb 13 23:50:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/02_2024/7wxw_32882_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/02_2024/7wxw_32882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/02_2024/7wxw_32882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/02_2024/7wxw_32882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/02_2024/7wxw_32882_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wxw_32882/02_2024/7wxw_32882_neut.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 52 5.16 5 C 5176 2.51 5 N 1407 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2179 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1942 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331} Time building chain proxies: 4.50, per 1000 atoms: 0.55 Number of scatterers: 8121 At special positions: 0 Unit cell: (84.7, 100.1, 133.1, 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 52 16.00 O 1486 8.00 N 1407 7.00 C 5176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 40.8% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'R' and resid 568 through 573 removed outlier: 3.978A pdb=" N LEU R 572 " --> pdb=" O PHE R 569 " (cutoff:3.500A) Processing helix chain 'R' and resid 581 through 610 removed outlier: 3.700A pdb=" N LYS R 586 " --> pdb=" O PHE R 582 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP R 587 " --> pdb=" O PRO R 583 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE R 588 " --> pdb=" O VAL R 584 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY R 594 " --> pdb=" O TYR R 590 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) Processing helix chain 'R' and resid 617 through 646 removed outlier: 3.712A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 655 through 687 removed outlier: 3.892A pdb=" N ALA R 659 " --> pdb=" O GLY R 655 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL R 661 " --> pdb=" O CYS R 657 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 707 removed outlier: 3.573A pdb=" N MET R 698 " --> pdb=" O ALA R 694 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 722 removed outlier: 3.556A pdb=" N ILE R 712 " --> pdb=" O GLY R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 723 through 725 No H-bonds generated for 'chain 'R' and resid 723 through 725' Processing helix chain 'R' and resid 744 through 767 Proline residue: R 750 - end of helix removed outlier: 3.607A pdb=" N ALA R 753 " --> pdb=" O VAL R 749 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE R 754 " --> pdb=" O PRO R 750 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL R 755 " --> pdb=" O ALA R 751 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL R 757 " --> pdb=" O ALA R 753 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL R 760 " --> pdb=" O ALA R 756 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 794 Processing helix chain 'R' and resid 795 through 801 removed outlier: 4.153A pdb=" N LEU R 799 " --> pdb=" O ILE R 795 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 800 " --> pdb=" O LEU R 796 " (cutoff:3.500A) Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 811 removed outlier: 3.969A pdb=" N THR R 810 " --> pdb=" O PHE R 806 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE R 811 " --> pdb=" O GLY R 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 806 through 811' Processing helix chain 'R' and resid 818 through 828 removed outlier: 3.654A pdb=" N PHE R 823 " --> pdb=" O TRP R 819 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA R 824 " --> pdb=" O HIS R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 854 removed outlier: 3.623A pdb=" N ARG R 846 " --> pdb=" O ASP R 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 44 removed outlier: 4.029A pdb=" N ALA C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.538A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.629A pdb=" N GLN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.780A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.676A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.547A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.993A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.677A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.710A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.640A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.669A pdb=" N ASN D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.734A pdb=" N LYS D 65 " --> pdb=" O GLY D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.551A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.684A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 6.379A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.646A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 83 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.125A pdb=" N GLY D 10 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 51 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 59 " --> pdb=" O ASP D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.917A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.147A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.698A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.074A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.992A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.943A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.126A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 3.00 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: 2636 1.34 - 1.46: 2015 1.46 - 1.59: 3567 1.59 - 1.71: 0 1.71 - 1.83: 74 Bond restraints: 8292 Sorted by residual: bond pdb=" CA GLY R 655 " pdb=" C GLY R 655 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.34e+00 bond pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 1.522 1.510 0.012 1.06e-02 8.90e+03 1.28e+00 bond pdb=" CG LEU D 20 " pdb=" CD1 LEU D 20 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CA HIS R 665 " pdb=" C HIS R 665 " ideal model delta sigma weight residual 1.524 1.510 0.014 1.28e-02 6.10e+03 1.23e+00 bond pdb=" N GLY R 655 " pdb=" CA GLY R 655 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.19e+00 ... (remaining 8287 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.16: 159 106.16 - 113.14: 4468 113.14 - 120.12: 3038 120.12 - 127.10: 3482 127.10 - 134.08: 91 Bond angle restraints: 11238 Sorted by residual: angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.70 128.85 -7.15 1.80e+00 3.09e-01 1.58e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 110.80 118.53 -7.73 2.13e+00 2.20e-01 1.32e+01 angle pdb=" N ALA B 104 " pdb=" CA ALA B 104 " pdb=" C ALA B 104 " ideal model delta sigma weight residual 108.46 113.90 -5.44 1.51e+00 4.39e-01 1.30e+01 angle pdb=" N TYR D 94 " pdb=" CA TYR D 94 " pdb=" C TYR D 94 " ideal model delta sigma weight residual 108.41 113.97 -5.56 1.63e+00 3.76e-01 1.16e+01 angle pdb=" N LYS A 17 " pdb=" CA LYS A 17 " pdb=" C LYS A 17 " ideal model delta sigma weight residual 111.07 107.44 3.63 1.07e+00 8.73e-01 1.15e+01 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 4559 18.16 - 36.32: 298 36.32 - 54.48: 44 54.48 - 72.64: 11 72.64 - 90.79: 7 Dihedral angle restraints: 4919 sinusoidal: 1930 harmonic: 2989 Sorted by residual: dihedral pdb=" CA GLN R 815 " pdb=" C GLN R 815 " pdb=" N ASN R 816 " pdb=" CA ASN R 816 " ideal model delta harmonic sigma weight residual -180.00 -138.00 -42.00 0 5.00e+00 4.00e-02 7.06e+01 dihedral pdb=" CB CYS R 657 " pdb=" SG CYS R 657 " pdb=" SG CYS R 733 " pdb=" CB CYS R 733 " ideal model delta sinusoidal sigma weight residual -86.00 -130.02 44.02 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA ALA B 104 " pdb=" C ALA B 104 " pdb=" N TYR B 105 " pdb=" CA TYR B 105 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1095 0.069 - 0.137: 171 0.137 - 0.206: 10 0.206 - 0.275: 3 0.275 - 0.343: 1 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA CYS R 657 " pdb=" N CYS R 657 " pdb=" C CYS R 657 " pdb=" CB CYS R 657 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1277 not shown) Planarity restraints: 1421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 666 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C PHE R 666 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE R 666 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE R 667 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 236 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 664 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C THR R 664 " 0.043 2.00e-02 2.50e+03 pdb=" O THR R 664 " -0.016 2.00e-02 2.50e+03 pdb=" N HIS R 665 " -0.015 2.00e-02 2.50e+03 ... (remaining 1418 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1854 2.78 - 3.31: 6917 3.31 - 3.84: 12032 3.84 - 4.37: 13717 4.37 - 4.90: 25112 Nonbonded interactions: 59632 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.256 2.440 nonbonded pdb=" OD1 ASP R 813 " pdb=" N SER R 814 " model vdw 2.264 2.520 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.315 2.440 nonbonded pdb=" OD1 ASP D 50 " pdb=" N ILE D 51 " model vdw 2.333 2.520 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.334 2.440 ... (remaining 59627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.850 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 24.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.005 0.044 8292 Z= 0.329 Angle : 0.779 8.363 11238 Z= 0.454 Chirality : 0.050 0.343 1280 Planarity : 0.006 0.066 1421 Dihedral : 12.888 90.794 2979 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.04 (0.23), residues: 1018 helix: -0.95 (0.26), residues: 356 sheet: -0.03 (0.36), residues: 197 loop : -2.27 (0.23), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.021 0.002 PHE R 569 TYR 0.021 0.002 TYR D 95 ARG 0.005 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: R 699 MET cc_start: 0.7298 (mmt) cc_final: 0.6984 (mpp) REVERT: R 724 SER cc_start: 0.6396 (t) cc_final: 0.6164 (t) REVERT: C 21 MET cc_start: 0.7263 (mtm) cc_final: 0.7018 (mtm) REVERT: A 309 GLU cc_start: 0.7047 (pm20) cc_final: 0.6650 (pm20) REVERT: A 378 ASP cc_start: 0.7463 (m-30) cc_final: 0.7213 (m-30) REVERT: B 45 MET cc_start: 0.8211 (mtp) cc_final: 0.8004 (mtp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 1.1582 time to fit residues: 235.7618 Evaluate side-chains 172 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 47 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.0370 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN A 29 GLN A 236 GLN B 88 ASN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8292 Z= 0.191 Angle : 0.553 7.672 11238 Z= 0.298 Chirality : 0.042 0.137 1280 Planarity : 0.004 0.059 1421 Dihedral : 4.963 42.219 1115 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.81 % Allowed : 10.51 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.96 (0.25), residues: 1018 helix: 0.47 (0.28), residues: 349 sheet: 0.29 (0.36), residues: 201 loop : -1.97 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE R 667 TYR 0.016 0.001 TYR D 95 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6719 (mpt) REVERT: R 724 SER cc_start: 0.6268 (t) cc_final: 0.6012 (t) REVERT: A 211 LYS cc_start: 0.8292 (mttp) cc_final: 0.8046 (mttt) REVERT: A 264 ASN cc_start: 0.8243 (t160) cc_final: 0.8039 (t0) REVERT: A 309 GLU cc_start: 0.7016 (pm20) cc_final: 0.6646 (pm20) REVERT: A 378 ASP cc_start: 0.7337 (m-30) cc_final: 0.6995 (m-30) REVERT: B 45 MET cc_start: 0.8215 (mtp) cc_final: 0.7988 (mtp) outliers start: 16 outliers final: 7 residues processed: 183 average time/residue: 1.2325 time to fit residues: 238.6123 Evaluate side-chains 176 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.0980 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 815 GLN C 59 ASN A 236 GLN B 176 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8292 Z= 0.152 Angle : 0.510 8.410 11238 Z= 0.269 Chirality : 0.041 0.130 1280 Planarity : 0.004 0.059 1421 Dihedral : 4.442 36.477 1115 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.60 % Allowed : 11.98 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1018 helix: 1.07 (0.28), residues: 350 sheet: 0.54 (0.36), residues: 208 loop : -1.77 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 667 TYR 0.019 0.001 TYR D 60 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: R 639 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6967 (t) REVERT: R 677 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7114 (mpp) REVERT: A 309 GLU cc_start: 0.6983 (pm20) cc_final: 0.6669 (pm20) REVERT: A 378 ASP cc_start: 0.7341 (m-30) cc_final: 0.7106 (m-30) REVERT: A 385 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6434 (mpt180) outliers start: 23 outliers final: 7 residues processed: 176 average time/residue: 1.2857 time to fit residues: 239.2416 Evaluate side-chains 177 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN D 31 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8292 Z= 0.208 Angle : 0.540 9.505 11238 Z= 0.286 Chirality : 0.042 0.141 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.462 35.464 1115 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.05 % Allowed : 13.33 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.20 (0.26), residues: 1018 helix: 1.25 (0.28), residues: 350 sheet: 0.77 (0.37), residues: 203 loop : -1.69 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE R 667 TYR 0.019 0.001 TYR D 60 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: R 677 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6864 (mpt) REVERT: A 252 ASP cc_start: 0.7193 (t0) cc_final: 0.6933 (p0) REVERT: A 309 GLU cc_start: 0.7003 (pm20) cc_final: 0.6652 (pm20) REVERT: A 378 ASP cc_start: 0.7368 (m-30) cc_final: 0.7139 (m-30) REVERT: A 385 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6327 (mpt180) outliers start: 27 outliers final: 20 residues processed: 175 average time/residue: 1.3455 time to fit residues: 248.4752 Evaluate side-chains 184 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 699 MET Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN D 31 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8292 Z= 0.274 Angle : 0.587 9.885 11238 Z= 0.308 Chirality : 0.043 0.147 1280 Planarity : 0.004 0.058 1421 Dihedral : 4.672 35.684 1115 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.50 % Allowed : 14.69 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.19 (0.26), residues: 1018 helix: 1.24 (0.28), residues: 350 sheet: 0.76 (0.35), residues: 220 loop : -1.77 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.021 0.002 PHE R 667 TYR 0.019 0.002 TYR D 60 ARG 0.004 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7694 (mp) cc_final: 0.7347 (tt) REVERT: R 677 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6799 (mpt) REVERT: R 688 LEU cc_start: 0.7952 (mt) cc_final: 0.7746 (mp) REVERT: R 766 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7185 (mp) REVERT: A 309 GLU cc_start: 0.7027 (pm20) cc_final: 0.6657 (pm20) REVERT: A 378 ASP cc_start: 0.7394 (m-30) cc_final: 0.7146 (m-30) REVERT: A 385 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.6315 (mpt180) outliers start: 31 outliers final: 22 residues processed: 176 average time/residue: 1.3230 time to fit residues: 245.6084 Evaluate side-chains 188 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 595 ILE Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 699 MET Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN D 31 ASN B 176 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8292 Z= 0.196 Angle : 0.537 9.392 11238 Z= 0.282 Chirality : 0.042 0.169 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.393 29.775 1115 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.84 % Allowed : 15.71 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.04 (0.26), residues: 1018 helix: 1.44 (0.28), residues: 350 sheet: 0.71 (0.35), residues: 224 loop : -1.69 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 667 TYR 0.021 0.001 TYR D 60 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7710 (mp) cc_final: 0.7389 (tt) REVERT: R 677 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7107 (mpp) REVERT: R 766 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7171 (mp) REVERT: A 309 GLU cc_start: 0.7009 (pm20) cc_final: 0.6625 (pm20) REVERT: A 378 ASP cc_start: 0.7361 (m-30) cc_final: 0.7127 (m-30) REVERT: A 385 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6314 (mpt180) REVERT: B 150 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8008 (mmt90) outliers start: 34 outliers final: 21 residues processed: 178 average time/residue: 1.3326 time to fit residues: 249.9278 Evaluate side-chains 186 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 687 ILE Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 721 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN D 31 ASN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8292 Z= 0.229 Angle : 0.562 9.605 11238 Z= 0.293 Chirality : 0.043 0.153 1280 Planarity : 0.004 0.058 1421 Dihedral : 4.432 25.966 1115 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.62 % Allowed : 15.59 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.04 (0.26), residues: 1018 helix: 1.40 (0.28), residues: 350 sheet: 0.71 (0.35), residues: 225 loop : -1.66 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE R 667 TYR 0.020 0.001 TYR D 60 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7743 (mp) cc_final: 0.7417 (tt) REVERT: R 677 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6813 (mpt) REVERT: R 766 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7199 (mp) REVERT: A 309 GLU cc_start: 0.7009 (pm20) cc_final: 0.6626 (pm20) REVERT: A 378 ASP cc_start: 0.7371 (m-30) cc_final: 0.7147 (m-30) REVERT: A 385 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6300 (mpt180) REVERT: B 150 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7990 (mmt90) outliers start: 32 outliers final: 20 residues processed: 176 average time/residue: 1.2528 time to fit residues: 232.7585 Evaluate side-chains 184 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 693 MET Chi-restraints excluded: chain R residue 721 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.0670 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.1980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 815 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8292 Z= 0.132 Angle : 0.498 9.113 11238 Z= 0.259 Chirality : 0.041 0.139 1280 Planarity : 0.004 0.054 1421 Dihedral : 3.991 21.801 1115 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.71 % Allowed : 17.63 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.22 (0.26), residues: 1018 helix: 1.70 (0.29), residues: 351 sheet: 0.72 (0.36), residues: 217 loop : -1.46 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE R 667 TYR 0.022 0.001 TYR D 60 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: R 639 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6944 (t) REVERT: R 677 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7119 (mpp) REVERT: R 766 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7074 (mp) REVERT: A 309 GLU cc_start: 0.6993 (pm20) cc_final: 0.6621 (pm20) REVERT: A 314 GLU cc_start: 0.6657 (mp0) cc_final: 0.6357 (mp0) REVERT: A 378 ASP cc_start: 0.7272 (m-30) cc_final: 0.7055 (m-30) REVERT: B 234 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8225 (m-80) outliers start: 24 outliers final: 13 residues processed: 177 average time/residue: 1.3062 time to fit residues: 243.7033 Evaluate side-chains 178 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 721 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0570 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 294 GLN D 31 ASN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 0.004 0.042 8292 Z= 0.275 Angle : 0.576 8.066 11238 Z= 0.304 Chirality : 0.043 0.149 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.398 22.528 1115 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.71 % Allowed : 18.08 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.10 (0.26), residues: 1018 helix: 1.52 (0.29), residues: 350 sheet: 0.79 (0.35), residues: 225 loop : -1.58 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE R 667 TYR 0.018 0.001 TYR D 60 ARG 0.004 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7724 (mp) cc_final: 0.7381 (tt) REVERT: R 677 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6788 (mpt) REVERT: R 766 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 309 GLU cc_start: 0.7016 (pm20) cc_final: 0.6626 (pm20) REVERT: A 378 ASP cc_start: 0.7372 (m-30) cc_final: 0.7135 (m-30) REVERT: B 150 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7999 (mmt90) REVERT: B 234 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8302 (m-80) outliers start: 24 outliers final: 15 residues processed: 174 average time/residue: 1.4308 time to fit residues: 263.4402 Evaluate side-chains 174 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 721 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN D 31 ASN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8292 Z= 0.231 Angle : 0.555 8.024 11238 Z= 0.293 Chirality : 0.042 0.142 1280 Planarity : 0.004 0.057 1421 Dihedral : 4.351 22.858 1115 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 18.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1018 helix: 1.51 (0.28), residues: 350 sheet: 0.80 (0.35), residues: 224 loop : -1.55 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE R 667 TYR 0.021 0.001 TYR D 60 ARG 0.004 0.000 ARG A 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: R 606 ILE cc_start: 0.7775 (mp) cc_final: 0.7438 (tt) REVERT: R 677 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6756 (mpt) REVERT: R 766 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7178 (mp) REVERT: A 309 GLU cc_start: 0.7007 (pm20) cc_final: 0.6618 (pm20) REVERT: A 378 ASP cc_start: 0.7375 (m-30) cc_final: 0.7133 (m-30) REVERT: D 83 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6759 (mtm) REVERT: B 150 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8007 (mmt90) REVERT: B 219 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7500 (mtm180) REVERT: B 234 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8248 (m-80) outliers start: 22 outliers final: 14 residues processed: 169 average time/residue: 1.4172 time to fit residues: 252.8117 Evaluate side-chains 175 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 639 VAL Chi-restraints excluded: chain R residue 677 MET Chi-restraints excluded: chain R residue 721 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 841 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 108 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN D 31 ASN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128788 restraints weight = 10807.298| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.31 r_work: 0.3539 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8292 Z= 0.214 Angle : 0.546 7.820 11238 Z= 0.288 Chirality : 0.042 0.141 1280 Planarity : 0.004 0.056 1421 Dihedral : 4.294 21.055 1115 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 18.31 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.15 (0.26), residues: 1018 helix: 1.56 (0.29), residues: 350 sheet: 0.81 (0.35), residues: 224 loop : -1.55 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE R 667 TYR 0.021 0.001 TYR D 60 ARG 0.004 0.000 ARG A 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4162.73 seconds wall clock time: 74 minutes 16.68 seconds (4456.68 seconds total)