Starting phenix.real_space_refine on Sat Sep 28 17:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzz_20541/09_2024/6pzz_20541.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzz_20541/09_2024/6pzz_20541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzz_20541/09_2024/6pzz_20541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzz_20541/09_2024/6pzz_20541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzz_20541/09_2024/6pzz_20541.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzz_20541/09_2024/6pzz_20541.cif" } resolution = 3.6 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= 0.090 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 124 5.16 5 C 12320 2.51 5 N 3348 2.21 5 O 3980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19772 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: G, J, L, C, B, D, I, H, K, O, Q, S, P, R, T Time building chain proxies: 8.67, per 1000 atoms: 0.44 Number of scatterers: 19772 At special positions: 0 Unit cell: (192.61, 192.61, 85.49, 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 124 16.00 O 3980 8.00 N 3348 7.00 C 12320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.02 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.02 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " NAG-ASN " NAG A 501 " - " ASN A 86 " " NAG B 501 " - " ASN B 86 " " NAG C 501 " - " ASN C 86 " " NAG D 501 " - " ASN D 86 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 200 " " NAG O 1 " - " ASN B 146 " " NAG P 1 " - " ASN B 200 " " NAG Q 1 " - " ASN C 146 " " NAG R 1 " - " ASN C 200 " " NAG S 1 " - " ASN D 146 " " NAG T 1 " - " ASN D 200 " Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.5 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 52 sheets defined 6.3% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 60 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 356 through 359 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.962A pdb=" N GLY A 90 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.660A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 125 removed outlier: 5.356A pdb=" N THR A 138 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ARG A 118 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN A 136 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU A 134 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL A 122 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 132 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS A 124 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 184 removed outlier: 5.709A pdb=" N TYR A 207 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 243 removed outlier: 3.561A pdb=" N LYS A 264 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ILE A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 282 removed outlier: 5.471A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.962A pdb=" N GLY B 90 " --> pdb=" O TYR B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.661A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 115 through 125 removed outlier: 5.355A pdb=" N THR B 138 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ARG B 118 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN B 136 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU B 134 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 122 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR B 132 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS B 124 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG B 130 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 179 through 184 removed outlier: 5.709A pdb=" N TYR B 207 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 236 through 243 removed outlier: 3.564A pdb=" N LYS B 264 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 282 removed outlier: 5.472A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.683A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.683A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.962A pdb=" N GLY C 90 " --> pdb=" O TYR C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.661A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA C 420 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 115 through 125 removed outlier: 5.355A pdb=" N THR C 138 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ARG C 118 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLN C 136 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU C 134 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL C 122 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR C 132 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS C 124 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG C 130 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 179 through 184 removed outlier: 5.707A pdb=" N TYR C 207 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 236 through 243 removed outlier: 3.562A pdb=" N LYS C 264 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 276 through 282 removed outlier: 5.472A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.685A pdb=" N LEU G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.961A pdb=" N GLY D 90 " --> pdb=" O TYR D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.661A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA D 420 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 115 through 125 removed outlier: 5.355A pdb=" N THR D 138 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ARG D 118 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLN D 136 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU D 134 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL D 122 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR D 132 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS D 124 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ARG D 130 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 179 through 184 removed outlier: 5.708A pdb=" N TYR D 207 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 236 through 243 removed outlier: 3.562A pdb=" N LYS D 264 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 276 through 282 removed outlier: 5.472A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 353 through 354 removed outlier: 6.186A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.684A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.684A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.809A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.626A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1536 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: 8.30 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3542 1.31 - 1.44: 6109 1.44 - 1.57: 10419 1.57 - 1.70: 38 1.70 - 1.83: 152 Bond restraints: 20260 Sorted by residual: bond pdb=" NE1 TRP D 161 " pdb=" CE2 TRP D 161 " ideal model delta sigma weight residual 1.370 1.289 0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" NE1 TRP B 161 " pdb=" CE2 TRP B 161 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.34e+01 bond pdb=" NE1 TRP A 161 " pdb=" CE2 TRP A 161 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.23e+01 bond pdb=" NE1 TRP C 161 " pdb=" CE2 TRP C 161 " ideal model delta sigma weight residual 1.370 1.290 0.080 1.10e-02 8.26e+03 5.22e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.543 -0.137 2.00e-02 2.50e+03 4.70e+01 ... (remaining 20255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 21543 2.03 - 4.07: 4791 4.07 - 6.10: 986 6.10 - 8.13: 200 8.13 - 10.16: 64 Bond angle restraints: 27584 Sorted by residual: angle pdb=" C GLY B 196 " pdb=" N PRO B 197 " pdb=" CA PRO B 197 " ideal model delta sigma weight residual 120.21 129.48 -9.27 9.60e-01 1.09e+00 9.32e+01 angle pdb=" C GLY C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 120.21 129.48 -9.27 9.60e-01 1.09e+00 9.32e+01 angle pdb=" C GLY A 196 " pdb=" N PRO A 197 " pdb=" CA PRO A 197 " ideal model delta sigma weight residual 120.21 129.45 -9.24 9.60e-01 1.09e+00 9.26e+01 angle pdb=" C GLY D 196 " pdb=" N PRO D 197 " pdb=" CA PRO D 197 " ideal model delta sigma weight residual 120.21 129.42 -9.21 9.60e-01 1.09e+00 9.20e+01 angle pdb=" C ASP D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta sigma weight residual 120.98 130.85 -9.87 1.07e+00 8.73e-01 8.50e+01 ... (remaining 27579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 12108 21.52 - 43.03: 331 43.03 - 64.55: 54 64.55 - 86.07: 44 86.07 - 107.58: 16 Dihedral angle restraints: 12553 sinusoidal: 5441 harmonic: 7112 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 132.98 -39.98 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 53.91 39.09 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" C ILE I 96 " pdb=" N ILE I 96 " pdb=" CA ILE I 96 " pdb=" CB ILE I 96 " ideal model delta harmonic sigma weight residual -122.00 -131.34 9.34 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 12550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2127 0.102 - 0.203: 821 0.203 - 0.305: 133 0.305 - 0.407: 31 0.407 - 0.508: 4 Chirality restraints: 3116 Sorted by residual: chirality pdb=" C1 MAN N 5 " pdb=" O2 MAN N 4 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.52e+01 chirality pdb=" C1 MAN P 5 " pdb=" O2 MAN P 4 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.43e+01 chirality pdb=" C1 MAN R 5 " pdb=" O2 MAN R 4 " pdb=" C2 MAN R 5 " pdb=" O5 MAN R 5 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-02 2.50e+03 5.10e+01 ... (remaining 3113 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 155 " -0.071 2.00e-02 2.50e+03 3.82e-02 2.91e+01 pdb=" CG TYR B 155 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 155 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR B 155 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 155 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 155 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 155 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 155 " 0.071 2.00e-02 2.50e+03 3.81e-02 2.90e+01 pdb=" CG TYR D 155 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR D 155 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 155 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR D 155 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR D 155 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR D 155 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 155 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 155 " -0.071 2.00e-02 2.50e+03 3.81e-02 2.90e+01 pdb=" CG TYR C 155 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR C 155 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR C 155 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR C 155 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR C 155 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR C 155 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 155 " -0.057 2.00e-02 2.50e+03 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 354 2.60 - 3.17: 17460 3.17 - 3.75: 32332 3.75 - 4.32: 47207 4.32 - 4.90: 75487 Nonbonded interactions: 172840 Sorted by model distance: nonbonded pdb=" SG CYS C 280 " pdb=" SG CYS C 289 " model vdw 2.021 3.760 nonbonded pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS B 280 " pdb=" SG CYS B 289 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS D 280 " pdb=" SG CYS D 289 " model vdw 2.022 3.760 nonbonded pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " model vdw 2.022 3.760 ... (remaining 172835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 44.800 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.024 0.159 20260 Z= 1.581 Angle : 1.885 10.162 27584 Z= 1.234 Chirality : 0.108 0.508 3116 Planarity : 0.009 0.042 3484 Dihedral : 12.057 107.584 7992 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: 0.57 (0.16), residues: 2440 helix: -0.45 (0.81), residues: 24 sheet: 0.79 (0.17), residues: 920 loop : 0.21 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP L 35 HIS 0.018 0.003 HIS A 274 PHE 0.029 0.008 PHE B 352 TYR 0.071 0.009 TYR B 155 ARG 0.007 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8263 (p) cc_final: 0.8037 (p) REVERT: B 168 THR cc_start: 0.8354 (p) cc_final: 0.8109 (p) REVERT: F 102 TYR cc_start: 0.8394 (m-80) cc_final: 0.7826 (m-80) REVERT: C 168 THR cc_start: 0.8338 (p) cc_final: 0.8100 (p) REVERT: D 168 THR cc_start: 0.8262 (p) cc_final: 0.8038 (p) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.3569 time to fit residues: 216.7253 Evaluate side-chains 183 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 226 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS B 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS C 226 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS D 226 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20260 Z= 0.259 Angle : 0.782 8.841 27584 Z= 0.399 Chirality : 0.049 0.337 3116 Planarity : 0.005 0.060 3484 Dihedral : 9.294 74.764 3672 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 1.89 % Allowed : 7.83 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.05 (0.16), residues: 2440 helix: 0.88 (1.01), residues: 24 sheet: 0.34 (0.16), residues: 972 loop : -0.25 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 206 HIS 0.004 0.001 HIS D 233 PHE 0.018 0.002 PHE J 96 TYR 0.028 0.002 TYR G 36 ARG 0.005 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8247 (p) cc_final: 0.7943 (p) REVERT: A 446 MET cc_start: 0.9091 (mmm) cc_final: 0.8474 (mmm) REVERT: L 39 LYS cc_start: 0.9044 (mttt) cc_final: 0.8835 (mttm) REVERT: L 55 GLN cc_start: 0.8121 (tp40) cc_final: 0.7653 (tp40) REVERT: H 69 MET cc_start: 0.8117 (mtt) cc_final: 0.7483 (mtt) REVERT: H 102 TYR cc_start: 0.7998 (m-80) cc_final: 0.7785 (m-80) REVERT: B 168 THR cc_start: 0.8234 (p) cc_final: 0.7944 (p) REVERT: E 55 GLN cc_start: 0.8037 (tp40) cc_final: 0.7709 (tp40) REVERT: F 69 MET cc_start: 0.8108 (mtt) cc_final: 0.7466 (mtt) REVERT: F 102 TYR cc_start: 0.8022 (m-80) cc_final: 0.7560 (m-80) REVERT: C 168 THR cc_start: 0.8225 (p) cc_final: 0.7937 (p) REVERT: C 446 MET cc_start: 0.9016 (mmm) cc_final: 0.8472 (mmm) REVERT: G 39 LYS cc_start: 0.9064 (mttt) cc_final: 0.8862 (mttm) REVERT: G 55 GLN cc_start: 0.8007 (tp40) cc_final: 0.7671 (tp40) REVERT: I 69 MET cc_start: 0.8101 (mtt) cc_final: 0.7458 (mtt) REVERT: D 168 THR cc_start: 0.8232 (p) cc_final: 0.7940 (p) REVERT: J 39 LYS cc_start: 0.9043 (mttt) cc_final: 0.8832 (mttm) REVERT: K 69 MET cc_start: 0.8099 (mtt) cc_final: 0.7470 (mtt) REVERT: K 102 TYR cc_start: 0.7964 (m-80) cc_final: 0.7733 (m-80) outliers start: 40 outliers final: 16 residues processed: 331 average time/residue: 0.2891 time to fit residues: 151.6939 Evaluate side-chains 237 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN L 37 GLN B 333 ASN E 37 GLN C 333 ASN D 333 ASN J 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 20260 Z= 0.568 Angle : 0.852 8.688 27584 Z= 0.426 Chirality : 0.050 0.260 3116 Planarity : 0.006 0.051 3484 Dihedral : 9.573 75.141 3672 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 2.55 % Allowed : 9.20 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.56 (0.16), residues: 2440 helix: -0.69 (0.85), residues: 24 sheet: -0.11 (0.16), residues: 960 loop : -0.49 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 103 HIS 0.009 0.002 HIS C 233 PHE 0.024 0.002 PHE L 96 TYR 0.028 0.003 TYR J 36 ARG 0.008 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 213 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 89 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8180 (tm-30) REVERT: H 69 MET cc_start: 0.8270 (mtt) cc_final: 0.7711 (mtt) REVERT: H 102 TYR cc_start: 0.8247 (m-80) cc_final: 0.8023 (m-80) REVERT: B 446 MET cc_start: 0.9173 (mmm) cc_final: 0.8446 (mmm) REVERT: E 89 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8528 (tm-30) REVERT: F 69 MET cc_start: 0.8248 (mtt) cc_final: 0.7697 (mtt) REVERT: C 446 MET cc_start: 0.9180 (mmm) cc_final: 0.8453 (mmm) REVERT: G 89 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8541 (tm-30) REVERT: I 69 MET cc_start: 0.8249 (mtt) cc_final: 0.7698 (mtt) REVERT: D 446 MET cc_start: 0.9190 (mmm) cc_final: 0.8460 (mmm) REVERT: J 89 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8570 (tm-30) REVERT: K 69 MET cc_start: 0.8250 (mtt) cc_final: 0.7700 (mtt) REVERT: K 102 TYR cc_start: 0.8193 (m-80) cc_final: 0.7961 (m-80) outliers start: 54 outliers final: 36 residues processed: 257 average time/residue: 0.2786 time to fit residues: 113.6829 Evaluate side-chains 208 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 37 GLN Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain I residue 50 TRP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN E 37 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20260 Z= 0.298 Angle : 0.687 8.580 27584 Z= 0.345 Chirality : 0.046 0.185 3116 Planarity : 0.005 0.048 3484 Dihedral : 8.764 65.866 3672 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Rotamer: Outliers : 2.78 % Allowed : 10.90 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.51 (0.16), residues: 2440 helix: -0.76 (0.80), residues: 24 sheet: 0.12 (0.17), residues: 916 loop : -0.60 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 103 HIS 0.003 0.001 HIS A 184 PHE 0.016 0.002 PHE J 96 TYR 0.022 0.002 TYR E 36 ARG 0.005 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 200 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.8187 (mtm) cc_final: 0.7983 (mtp) REVERT: L 6 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: L 42 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8115 (mmmm) REVERT: H 69 MET cc_start: 0.8208 (mtt) cc_final: 0.7658 (mtt) REVERT: B 446 MET cc_start: 0.9183 (mmm) cc_final: 0.8510 (mmm) REVERT: E 6 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7855 (mt0) REVERT: E 39 LYS cc_start: 0.9078 (mttm) cc_final: 0.8876 (mttp) REVERT: E 89 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8302 (tm-30) REVERT: F 69 MET cc_start: 0.8180 (mtt) cc_final: 0.7644 (mtt) REVERT: C 446 MET cc_start: 0.9174 (mmm) cc_final: 0.8514 (mmm) REVERT: G 6 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: G 42 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8118 (mmmm) REVERT: G 89 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8286 (tm-30) REVERT: I 69 MET cc_start: 0.8184 (mtt) cc_final: 0.7640 (mtt) REVERT: D 446 MET cc_start: 0.9200 (mmm) cc_final: 0.8490 (mmm) REVERT: J 6 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: J 42 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8127 (mmmm) REVERT: J 89 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8263 (tm-30) REVERT: K 69 MET cc_start: 0.8180 (mtt) cc_final: 0.7639 (mtt) REVERT: K 102 TYR cc_start: 0.8164 (m-80) cc_final: 0.7949 (m-80) outliers start: 59 outliers final: 41 residues processed: 248 average time/residue: 0.2784 time to fit residues: 110.7639 Evaluate side-chains 221 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.6980 chunk 131 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN E 37 GLN J 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20260 Z= 0.180 Angle : 0.626 7.878 27584 Z= 0.315 Chirality : 0.045 0.174 3116 Planarity : 0.004 0.046 3484 Dihedral : 8.082 59.393 3672 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.39 % Rotamer: Outliers : 2.31 % Allowed : 11.37 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.41 (0.17), residues: 2440 helix: -1.37 (0.75), residues: 24 sheet: 0.26 (0.17), residues: 916 loop : -0.57 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 456 HIS 0.003 0.001 HIS A 184 PHE 0.013 0.001 PHE L 96 TYR 0.021 0.002 TYR E 92 ARG 0.005 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9172 (mmm) cc_final: 0.8578 (mmm) REVERT: L 6 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: L 70 ASP cc_start: 0.8291 (m-30) cc_final: 0.8066 (p0) REVERT: H 69 MET cc_start: 0.8212 (mtt) cc_final: 0.7991 (mmt) REVERT: B 237 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8342 (m) REVERT: E 6 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: E 70 ASP cc_start: 0.8416 (m-30) cc_final: 0.8195 (p0) REVERT: F 69 MET cc_start: 0.8178 (mtt) cc_final: 0.7686 (mtt) REVERT: F 80 MET cc_start: 0.7973 (tmm) cc_final: 0.7660 (ppp) REVERT: F 91 TYR cc_start: 0.8729 (m-80) cc_final: 0.8074 (m-80) REVERT: C 237 CYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8352 (m) REVERT: G 6 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: G 70 ASP cc_start: 0.8422 (m-30) cc_final: 0.8220 (p0) REVERT: I 69 MET cc_start: 0.8184 (mtt) cc_final: 0.7671 (mtt) REVERT: I 80 MET cc_start: 0.7992 (tmm) cc_final: 0.7672 (ppp) REVERT: I 91 TYR cc_start: 0.8743 (m-80) cc_final: 0.8110 (m-80) REVERT: D 237 CYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (m) REVERT: J 6 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7791 (mt0) REVERT: K 69 MET cc_start: 0.8183 (mtt) cc_final: 0.7679 (mtt) REVERT: K 80 MET cc_start: 0.8025 (tmm) cc_final: 0.7675 (ppp) REVERT: K 91 TYR cc_start: 0.8736 (m-80) cc_final: 0.8180 (m-80) outliers start: 49 outliers final: 32 residues processed: 253 average time/residue: 0.2982 time to fit residues: 119.0456 Evaluate side-chains 212 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN B 226 GLN C 226 GLN G 37 GLN D 226 GLN J 37 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20260 Z= 0.412 Angle : 0.707 7.960 27584 Z= 0.354 Chirality : 0.047 0.185 3116 Planarity : 0.005 0.052 3484 Dihedral : 8.329 60.751 3672 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.34 % Rotamer: Outliers : 2.97 % Allowed : 11.75 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.54 (0.17), residues: 2440 helix: -1.37 (0.85), residues: 24 sheet: 0.17 (0.17), residues: 904 loop : -0.65 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 456 HIS 0.005 0.001 HIS C 233 PHE 0.012 0.002 PHE L 96 TYR 0.019 0.002 TYR G 36 ARG 0.006 0.001 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 188 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9244 (mmm) cc_final: 0.9016 (mmm) REVERT: L 6 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: H 69 MET cc_start: 0.8202 (mtt) cc_final: 0.7690 (mtt) REVERT: B 237 CYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8389 (m) REVERT: E 6 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: F 69 MET cc_start: 0.8158 (mtt) cc_final: 0.7654 (mtt) REVERT: C 237 CYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8408 (m) REVERT: C 446 MET cc_start: 0.9253 (mmm) cc_final: 0.9008 (mmm) REVERT: G 6 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: I 69 MET cc_start: 0.8213 (mtt) cc_final: 0.7705 (mtt) REVERT: D 237 CYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8391 (m) REVERT: J 6 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: K 69 MET cc_start: 0.8197 (mtt) cc_final: 0.7675 (mtt) outliers start: 63 outliers final: 40 residues processed: 240 average time/residue: 0.2680 time to fit residues: 104.9997 Evaluate side-chains 219 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 169 optimal weight: 50.0000 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN G 37 GLN J 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20260 Z= 0.348 Angle : 0.692 8.015 27584 Z= 0.345 Chirality : 0.046 0.183 3116 Planarity : 0.005 0.051 3484 Dihedral : 8.084 57.675 3672 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.47 % Rotamer: Outliers : 2.31 % Allowed : 12.92 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.64 (0.17), residues: 2440 helix: -1.29 (0.86), residues: 24 sheet: 0.13 (0.17), residues: 908 loop : -0.75 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 456 HIS 0.004 0.001 HIS A 184 PHE 0.036 0.002 PHE L 62 TYR 0.021 0.002 TYR G 36 ARG 0.005 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9227 (mmm) cc_final: 0.8991 (mmm) REVERT: L 6 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: L 79 GLN cc_start: 0.7714 (pt0) cc_final: 0.7388 (pt0) REVERT: H 69 MET cc_start: 0.8223 (mtt) cc_final: 0.7708 (mtt) REVERT: B 237 CYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8382 (m) REVERT: E 6 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: F 69 MET cc_start: 0.8122 (mtt) cc_final: 0.7603 (mtt) REVERT: C 237 CYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8396 (m) REVERT: C 446 MET cc_start: 0.9250 (mmm) cc_final: 0.9016 (mmm) REVERT: G 6 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: I 69 MET cc_start: 0.8141 (mtt) cc_final: 0.7624 (mtt) REVERT: D 237 CYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8380 (m) REVERT: J 6 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: J 79 GLN cc_start: 0.7675 (pt0) cc_final: 0.7370 (pt0) REVERT: K 69 MET cc_start: 0.8165 (mtt) cc_final: 0.7661 (mtt) outliers start: 49 outliers final: 36 residues processed: 228 average time/residue: 0.2756 time to fit residues: 101.1172 Evaluate side-chains 212 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20260 Z= 0.265 Angle : 0.658 7.696 27584 Z= 0.328 Chirality : 0.045 0.184 3116 Planarity : 0.004 0.049 3484 Dihedral : 7.684 53.837 3672 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 2.26 % Allowed : 13.40 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.59 (0.17), residues: 2440 helix: -1.28 (0.81), residues: 24 sheet: 0.22 (0.17), residues: 908 loop : -0.76 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 456 HIS 0.003 0.001 HIS A 184 PHE 0.011 0.001 PHE L 96 TYR 0.029 0.002 TYR K 27 ARG 0.005 0.001 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 195 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9247 (mmm) cc_final: 0.9041 (mmm) REVERT: L 6 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: H 69 MET cc_start: 0.8208 (mtt) cc_final: 0.7707 (mtt) REVERT: B 237 CYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8395 (m) REVERT: B 446 MET cc_start: 0.9122 (mmm) cc_final: 0.8606 (mmm) REVERT: E 6 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: F 69 MET cc_start: 0.8178 (mtt) cc_final: 0.7700 (mtt) REVERT: C 237 CYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8399 (m) REVERT: C 446 MET cc_start: 0.9205 (mmm) cc_final: 0.8983 (mmm) REVERT: G 6 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: I 69 MET cc_start: 0.8150 (mtt) cc_final: 0.7661 (mtt) REVERT: D 237 CYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8399 (m) REVERT: D 446 MET cc_start: 0.9128 (mmm) cc_final: 0.8627 (mmm) REVERT: J 6 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: K 69 MET cc_start: 0.8184 (mtt) cc_final: 0.7677 (mtt) outliers start: 48 outliers final: 38 residues processed: 235 average time/residue: 0.2714 time to fit residues: 103.5903 Evaluate side-chains 215 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20260 Z= 0.385 Angle : 0.717 9.080 27584 Z= 0.355 Chirality : 0.047 0.187 3116 Planarity : 0.005 0.053 3484 Dihedral : 7.850 54.538 3672 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.15 % Favored : 93.69 % Rotamer: Outliers : 2.31 % Allowed : 13.11 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.80 (0.17), residues: 2440 helix: -1.27 (0.85), residues: 24 sheet: -0.12 (0.16), residues: 960 loop : -0.77 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 361 HIS 0.005 0.001 HIS B 184 PHE 0.013 0.002 PHE L 96 TYR 0.022 0.002 TYR E 36 ARG 0.006 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9255 (mmm) cc_final: 0.9017 (mmm) REVERT: L 6 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: H 69 MET cc_start: 0.8241 (mtt) cc_final: 0.7745 (mtt) REVERT: B 237 CYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8395 (m) REVERT: E 6 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: F 69 MET cc_start: 0.8195 (mtt) cc_final: 0.7701 (mtt) REVERT: C 237 CYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8411 (m) REVERT: C 446 MET cc_start: 0.9235 (mmm) cc_final: 0.8988 (mmm) REVERT: G 6 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: I 69 MET cc_start: 0.8166 (mtt) cc_final: 0.7656 (mtt) REVERT: D 237 CYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8388 (m) REVERT: J 6 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7964 (mt0) REVERT: K 69 MET cc_start: 0.8180 (mtt) cc_final: 0.7676 (mtt) outliers start: 49 outliers final: 37 residues processed: 216 average time/residue: 0.2756 time to fit residues: 97.2995 Evaluate side-chains 208 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20260 Z= 0.317 Angle : 0.704 9.845 27584 Z= 0.348 Chirality : 0.047 0.186 3116 Planarity : 0.005 0.052 3484 Dihedral : 7.582 51.705 3672 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 2.12 % Allowed : 13.49 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.81 (0.17), residues: 2440 helix: -1.30 (0.81), residues: 24 sheet: -0.10 (0.17), residues: 960 loop : -0.81 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 456 HIS 0.004 0.001 HIS B 184 PHE 0.012 0.002 PHE L 96 TYR 0.021 0.002 TYR E 36 ARG 0.005 0.001 ARG J 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 446 MET cc_start: 0.9263 (mmm) cc_final: 0.9048 (mmm) REVERT: L 6 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: L 89 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8728 (tm-30) REVERT: H 69 MET cc_start: 0.8196 (mtt) cc_final: 0.7726 (mtt) REVERT: B 237 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8377 (m) REVERT: E 6 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: E 89 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8420 (tm-30) REVERT: F 69 MET cc_start: 0.8189 (mtt) cc_final: 0.7730 (mtt) REVERT: C 237 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8397 (m) REVERT: C 446 MET cc_start: 0.9232 (mmm) cc_final: 0.9006 (mmm) REVERT: G 6 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: G 89 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8437 (tm-30) REVERT: I 69 MET cc_start: 0.8211 (mtt) cc_final: 0.7725 (mtt) REVERT: D 237 CYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8359 (m) REVERT: J 6 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: K 69 MET cc_start: 0.8177 (mtt) cc_final: 0.7680 (mtt) outliers start: 45 outliers final: 38 residues processed: 227 average time/residue: 0.2597 time to fit residues: 97.7330 Evaluate side-chains 219 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 237 CYS Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 CYS Chi-restraints excluded: chain D residue 442 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 23 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 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 = 0.3166 r_free = 0.3166 target = 0.066805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053290 restraints weight = 62857.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.055203 restraints weight = 26361.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056415 restraints weight = 14896.935| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20260 Z= 0.335 Angle : 0.725 14.155 27584 Z= 0.354 Chirality : 0.047 0.185 3116 Planarity : 0.005 0.052 3484 Dihedral : 7.540 51.052 3672 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.82 % Favored : 94.02 % Rotamer: Outliers : 2.12 % Allowed : 13.82 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -0.89 (0.17), residues: 2440 helix: -1.34 (0.81), residues: 24 sheet: -0.15 (0.16), residues: 960 loop : -0.86 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 456 HIS 0.005 0.001 HIS B 98 PHE 0.012 0.002 PHE J 96 TYR 0.024 0.002 TYR E 36 ARG 0.005 0.001 ARG J 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.66 seconds wall clock time: 64 minutes 53.86 seconds (3893.86 seconds total)