Starting phenix.real_space_refine on Sat Dec 28 06:28:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8daq_27272/12_2024/8daq_27272.cif Found real_map, /net/cci-nas-00/data/ceres_data/8daq_27272/12_2024/8daq_27272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8daq_27272/12_2024/8daq_27272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8daq_27272/12_2024/8daq_27272.map" model { file = "/net/cci-nas-00/data/ceres_data/8daq_27272/12_2024/8daq_27272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8daq_27272/12_2024/8daq_27272.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 164 5.16 5 C 16708 2.51 5 N 4520 2.21 5 O 4944 1.98 5 H 25764 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 52100 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6568 Classifications: {'peptide': 438} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "B" Number of atoms: 6429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6429 Classifications: {'peptide': 415} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 386} 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 Chain: "B" 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: D, F, H, C, E, G Time building chain proxies: 22.28, per 1000 atoms: 0.43 Number of scatterers: 52100 At special positions: 0 Unit cell: (182.4, 160.8, 172.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 164 16.00 O 4944 8.00 N 4520 7.00 C 16708 6.00 H 25764 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.03 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 NAG-ASN " NAG A 501 " - " ASN A 139 " " NAG B 501 " - " ASN B 199 " " NAG C 501 " - " ASN C 139 " " NAG D 501 " - " ASN D 199 " " NAG E 501 " - " ASN E 139 " " NAG F 501 " - " ASN F 199 " " NAG G 501 " - " ASN G 139 " " NAG H 501 " - " ASN H 199 " Time building additional restraints: 10.18 Conformation dependent library (CDL) restraints added in 3.2 seconds 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 77 sheets defined 13.4% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.506A pdb=" N MET A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.136A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.960A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.572A pdb=" N TYR B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 401 removed outlier: 4.138A pdb=" N LEU B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.507A pdb=" N MET C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.136A pdb=" N GLY C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 403 through 414 Processing helix chain 'C' and resid 416 through 438 removed outlier: 3.960A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 358 through 365 removed outlier: 3.571A pdb=" N TYR D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 401 removed outlier: 4.138A pdb=" N LEU D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 419 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 238 through 246 removed outlier: 3.506A pdb=" N MET E 242 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 255 through 259 removed outlier: 4.136A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS E 259 " --> pdb=" O PRO E 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 255 through 259' Processing helix chain 'E' and resid 403 through 414 Processing helix chain 'E' and resid 416 through 438 removed outlier: 3.960A pdb=" N LEU E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 438 " --> pdb=" O LEU E 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 358 through 365 removed outlier: 3.571A pdb=" N TYR F 362 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 401 removed outlier: 4.138A pdb=" N LEU F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 419 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.506A pdb=" N MET G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.135A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 403 through 414 Processing helix chain 'G' and resid 416 through 438 removed outlier: 3.961A pdb=" N LEU G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 438 " --> pdb=" O LEU G 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 179 through 181 No H-bonds generated for 'chain 'H' and resid 179 through 181' Processing helix chain 'H' and resid 358 through 365 removed outlier: 3.571A pdb=" N TYR H 362 " --> pdb=" O ILE H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 401 removed outlier: 4.138A pdb=" N LEU H 374 " --> pdb=" O THR H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 21 removed outlier: 3.577A pdb=" N LEU A 27 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG A 21 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 147 removed outlier: 6.556A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 removed outlier: 3.580A pdb=" N VAL A 214 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 306 removed outlier: 4.316A pdb=" N VAL A 299 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN A 319 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS A 301 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR A 317 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N VAL A 303 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER A 315 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.818A pdb=" N THR A 344 " --> pdb=" O CYS A 328 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS A 328 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.024A pdb=" N GLN B 107 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG B 96 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.850A pdb=" N TYR B 72 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89 removed outlier: 4.155A pdb=" N ASP B 112 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 158 Processing sheet with id=AB6, first strand: chain 'B' and resid 166 through 171 removed outlier: 5.609A pdb=" N GLY B 167 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE B 260 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 213 removed outlier: 3.939A pdb=" N THR B 201 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AC1, first strand: chain 'B' and resid 296 through 300 Processing sheet with id=AC2, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AC3, first strand: chain 'C' and resid 15 through 21 removed outlier: 3.577A pdb=" N LEU C 27 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 21 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 45 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 47 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 141 through 147 removed outlier: 6.555A pdb=" N VAL C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 47 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 45 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN C 43 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR C 126 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 134 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL C 33 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL C 136 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE C 31 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR C 107 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR C 107 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC8, first strand: chain 'C' and resid 203 through 204 removed outlier: 3.580A pdb=" N VAL C 214 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 296 through 306 removed outlier: 4.315A pdb=" N VAL C 299 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN C 319 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N CYS C 301 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 317 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL C 303 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N SER C 315 " --> pdb=" O VAL C 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 343 through 345 removed outlier: 3.819A pdb=" N THR C 344 " --> pdb=" O CYS C 328 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS C 328 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AD3, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.024A pdb=" N GLN D 107 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG D 96 " --> pdb=" O GLN D 107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.850A pdb=" N TYR D 72 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.155A pdb=" N ASP D 112 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 151 through 158 Processing sheet with id=AD7, first strand: chain 'D' and resid 166 through 171 removed outlier: 5.609A pdb=" N GLY D 167 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE D 260 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AD9, first strand: chain 'D' and resid 210 through 213 removed outlier: 3.939A pdb=" N THR D 201 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AE2, first strand: chain 'D' and resid 296 through 300 Processing sheet with id=AE3, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AE4, first strand: chain 'E' and resid 15 through 21 removed outlier: 3.578A pdb=" N LEU E 27 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG E 21 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE E 31 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR E 126 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN E 43 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU E 45 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 47 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 141 through 147 removed outlier: 6.556A pdb=" N VAL E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E 47 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU E 45 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN E 43 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N THR E 126 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE E 31 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR E 107 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR E 107 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'E' and resid 203 through 204 removed outlier: 3.580A pdb=" N VAL E 214 " --> pdb=" O GLN E 204 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 296 through 306 removed outlier: 4.315A pdb=" N VAL E 299 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN E 319 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N CYS E 301 " --> pdb=" O THR E 317 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR E 317 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL E 303 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER E 315 " --> pdb=" O VAL E 303 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 343 through 345 removed outlier: 3.818A pdb=" N THR E 344 " --> pdb=" O CYS E 328 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS E 328 " --> pdb=" O THR E 344 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AF4, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AF5, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.024A pdb=" N GLN F 107 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG F 96 " --> pdb=" O GLN F 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.850A pdb=" N TYR F 72 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.154A pdb=" N ASP F 112 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 151 through 158 Processing sheet with id=AF9, first strand: chain 'F' and resid 166 through 171 removed outlier: 5.610A pdb=" N GLY F 167 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE F 260 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 183 through 184 Processing sheet with id=AG2, first strand: chain 'F' and resid 210 through 213 removed outlier: 3.939A pdb=" N THR F 201 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 278 through 279 Processing sheet with id=AG4, first strand: chain 'F' and resid 296 through 300 Processing sheet with id=AG5, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AG6, first strand: chain 'G' and resid 15 through 21 removed outlier: 3.577A pdb=" N LEU G 27 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 141 through 147 removed outlier: 6.556A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.763A pdb=" N TYR G 107 " --> pdb=" O VAL G 54 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AH2, first strand: chain 'G' and resid 203 through 204 removed outlier: 3.579A pdb=" N VAL G 214 " --> pdb=" O GLN G 204 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 296 through 306 removed outlier: 4.315A pdb=" N VAL G 299 " --> pdb=" O GLN G 319 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN G 319 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS G 301 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR G 317 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL G 303 " --> pdb=" O SER G 315 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER G 315 " --> pdb=" O VAL G 303 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 343 through 345 removed outlier: 3.819A pdb=" N THR G 344 " --> pdb=" O CYS G 328 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS G 328 " --> pdb=" O THR G 344 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AH6, first strand: chain 'H' and resid 37 through 38 removed outlier: 6.024A pdb=" N GLN H 107 " --> pdb=" O ARG H 96 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG H 96 " --> pdb=" O GLN H 107 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.850A pdb=" N TYR H 72 " --> pdb=" O LYS H 79 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 86 through 89 removed outlier: 4.154A pdb=" N ASP H 112 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 151 through 158 Processing sheet with id=AI1, first strand: chain 'H' and resid 166 through 171 removed outlier: 5.609A pdb=" N GLY H 167 " --> pdb=" O ILE H 260 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE H 260 " --> pdb=" O GLY H 167 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 183 through 184 Processing sheet with id=AI3, first strand: chain 'H' and resid 210 through 213 removed outlier: 3.939A pdb=" N THR H 201 " --> pdb=" O TYR H 232 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 278 through 279 Processing sheet with id=AI5, first strand: chain 'H' and resid 296 through 300 842 hydrogen bonds defined for protein. 2199 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: 17.85 Time building geometry restraints manager: 12.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 25764 1.04 - 1.24: 2429 1.24 - 1.43: 9199 1.43 - 1.63: 15208 1.63 - 1.83: 196 Bond restraints: 52796 Sorted by residual: bond pdb=" N PHE A 1 " pdb=" H2 PHE A 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N PHE E 1 " pdb=" H3 PHE E 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N ILE D 5 " pdb=" H2 ILE D 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N ILE F 5 " pdb=" H3 ILE F 5 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N PHE C 1 " pdb=" H3 PHE C 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 52791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.05: 95484 15.05 - 30.10: 8 30.10 - 45.15: 12 45.15 - 60.21: 4 60.21 - 75.26: 4 Bond angle restraints: 95512 Sorted by residual: angle pdb=" H1 ILE H 5 " pdb=" N ILE H 5 " pdb=" H2 ILE H 5 " ideal model delta sigma weight residual 109.47 34.21 75.26 3.00e+00 1.11e-01 6.29e+02 angle pdb=" H1 ILE B 5 " pdb=" N ILE B 5 " pdb=" H2 ILE B 5 " ideal model delta sigma weight residual 109.47 34.21 75.26 3.00e+00 1.11e-01 6.29e+02 angle pdb=" H1 ILE D 5 " pdb=" N ILE D 5 " pdb=" H2 ILE D 5 " ideal model delta sigma weight residual 109.47 34.24 75.23 3.00e+00 1.11e-01 6.29e+02 angle pdb=" H1 ILE F 5 " pdb=" N ILE F 5 " pdb=" H2 ILE F 5 " ideal model delta sigma weight residual 109.47 34.30 75.17 3.00e+00 1.11e-01 6.28e+02 angle pdb=" H1 PHE C 1 " pdb=" N PHE C 1 " pdb=" H2 PHE C 1 " ideal model delta sigma weight residual 109.47 50.17 59.30 3.00e+00 1.11e-01 3.91e+02 ... (remaining 95507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 22764 17.93 - 35.87: 1832 35.87 - 53.80: 583 53.80 - 71.74: 123 71.74 - 89.67: 32 Dihedral angle restraints: 25334 sinusoidal: 13594 harmonic: 11740 Sorted by residual: dihedral pdb=" CB CYS B 206 " pdb=" SG CYS B 206 " pdb=" SG CYS B 223 " pdb=" CB CYS B 223 " ideal model delta sinusoidal sigma weight residual -86.00 -36.81 -49.19 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 28 " pdb=" CB CYS B 28 " ideal model delta sinusoidal sigma weight residual -86.00 -122.22 36.22 1 1.00e+01 1.00e-02 1.86e+01 dihedral pdb=" CA VAL E 226 " pdb=" C VAL E 226 " pdb=" N LYS E 227 " pdb=" CA LYS E 227 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 25331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3716 0.070 - 0.140: 477 0.140 - 0.210: 15 0.210 - 0.279: 0 0.279 - 0.349: 4 Chirality restraints: 4212 Sorted by residual: chirality pdb=" CA ASN H 199 " pdb=" N ASN H 199 " pdb=" C ASN H 199 " pdb=" CB ASN H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA ASN B 199 " pdb=" N ASN B 199 " pdb=" C ASN B 199 " pdb=" CB ASN B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASN F 199 " pdb=" N ASN F 199 " pdb=" C ASN F 199 " pdb=" CB ASN F 199 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 4209 not shown) Planarity restraints: 7892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 411 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO D 412 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 411 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO H 412 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 412 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 412 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 411 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO F 412 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO F 412 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 412 " -0.033 5.00e-02 4.00e+02 ... (remaining 7889 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1221 2.07 - 2.70: 86465 2.70 - 3.34: 149766 3.34 - 3.97: 186664 3.97 - 4.60: 280616 Nonbonded interactions: 704732 Sorted by model distance: nonbonded pdb=" O GLY A 90 " pdb=" H LYS B 180 " model vdw 1.439 2.450 nonbonded pdb=" O THR B 276 " pdb="HH22 ARG E 220 " model vdw 1.454 2.450 nonbonded pdb=" OE1 GLU E 390 " pdb=" H GLU E 390 " model vdw 1.499 2.450 nonbonded pdb=" OE1 GLU A 390 " pdb=" H GLU A 390 " model vdw 1.499 2.450 nonbonded pdb=" OE1 GLU C 390 " pdb=" H GLU C 390 " model vdw 1.500 2.450 ... (remaining 704727 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 0.830 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: 0.710 Extract box with map and model: 1.430 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 86.520 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 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 : 0.003 0.055 27032 Z= 0.191 Angle : 0.562 5.702 36860 Z= 0.303 Chirality : 0.045 0.349 4212 Planarity : 0.004 0.061 4700 Dihedral : 13.373 89.674 9816 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3396 helix: 1.73 (0.28), residues: 340 sheet: -0.86 (0.16), residues: 988 loop : -1.43 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 282 HIS 0.006 0.001 HIS H 275 PHE 0.013 0.001 PHE B 29 TYR 0.012 0.001 TYR D 102 ARG 0.004 0.000 ARG F 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7015 (mp10) cc_final: 0.6337 (tm-30) REVERT: A 254 THR cc_start: 0.7717 (p) cc_final: 0.7381 (p) REVERT: A 353 THR cc_start: 0.6005 (m) cc_final: 0.5768 (p) REVERT: C 152 THR cc_start: 0.7614 (t) cc_final: 0.7403 (p) REVERT: D 297 LEU cc_start: 0.8031 (tp) cc_final: 0.7827 (tp) REVERT: E 66 LEU cc_start: 0.8223 (mt) cc_final: 0.7139 (mt) REVERT: G 27 LEU cc_start: 0.4929 (tt) cc_final: 0.4609 (tt) REVERT: G 353 THR cc_start: 0.7232 (m) cc_final: 0.7011 (p) REVERT: H 144 LEU cc_start: 0.7999 (tp) cc_final: 0.7526 (tp) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.7195 time to fit residues: 751.8358 Evaluate side-chains 430 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 305 optimal weight: 0.7980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS B 156 HIS B 356 HIS ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 HIS E 364 ASN G 175 HIS H 24 HIS H 58 GLN ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27032 Z= 0.274 Angle : 0.605 6.301 36860 Z= 0.322 Chirality : 0.044 0.330 4212 Planarity : 0.006 0.065 4700 Dihedral : 5.017 24.426 3856 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3396 helix: 1.46 (0.28), residues: 364 sheet: -1.31 (0.15), residues: 1132 loop : -1.47 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 38 HIS 0.009 0.001 HIS D 275 PHE 0.033 0.002 PHE G 287 TYR 0.013 0.001 TYR D 102 ARG 0.004 0.001 ARG C 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 499 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7202 (mp10) cc_final: 0.6719 (tm-30) REVERT: D 297 LEU cc_start: 0.8153 (tp) cc_final: 0.7908 (tp) REVERT: E 221 LEU cc_start: 0.8075 (mm) cc_final: 0.7805 (mm) outliers start: 1 outliers final: 0 residues processed: 500 average time/residue: 0.6891 time to fit residues: 542.0557 Evaluate side-chains 387 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 305 optimal weight: 0.7980 chunk 330 optimal weight: 0.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 HIS E 345 HIS E 364 ASN G 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27032 Z= 0.195 Angle : 0.553 6.017 36860 Z= 0.293 Chirality : 0.045 0.335 4212 Planarity : 0.005 0.057 4700 Dihedral : 4.849 22.718 3856 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3396 helix: 1.54 (0.28), residues: 364 sheet: -1.26 (0.15), residues: 1124 loop : -1.36 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 89 HIS 0.016 0.001 HIS H 361 PHE 0.017 0.001 PHE G 398 TYR 0.012 0.001 TYR D 102 ARG 0.006 0.000 ARG F 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 252 GLN cc_start: 0.7060 (mp10) cc_final: 0.6518 (tm-30) REVERT: D 297 LEU cc_start: 0.8015 (tp) cc_final: 0.7793 (tp) REVERT: E 221 LEU cc_start: 0.8117 (mm) cc_final: 0.7756 (mm) REVERT: F 297 LEU cc_start: 0.7477 (tp) cc_final: 0.7272 (tp) outliers start: 1 outliers final: 0 residues processed: 493 average time/residue: 0.6658 time to fit residues: 518.9436 Evaluate side-chains 393 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 290 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27032 Z= 0.337 Angle : 0.621 6.555 36860 Z= 0.334 Chirality : 0.044 0.343 4212 Planarity : 0.005 0.051 4700 Dihedral : 5.233 25.577 3856 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3396 helix: 1.25 (0.28), residues: 368 sheet: -1.45 (0.15), residues: 1124 loop : -1.56 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 38 HIS 0.013 0.002 HIS G 392 PHE 0.030 0.002 PHE B 9 TYR 0.027 0.002 TYR F 21 ARG 0.013 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ILE cc_start: 0.4904 (pt) cc_final: 0.4396 (pt) REVERT: A 369 LEU cc_start: 0.7545 (tt) cc_final: 0.7107 (tt) REVERT: B 144 LEU cc_start: 0.8282 (tt) cc_final: 0.7874 (tt) REVERT: D 145 PHE cc_start: 0.7707 (m-80) cc_final: 0.7473 (m-80) REVERT: D 297 LEU cc_start: 0.8193 (tp) cc_final: 0.7987 (tp) REVERT: E 221 LEU cc_start: 0.8137 (mm) cc_final: 0.7786 (mm) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.6600 time to fit residues: 466.7611 Evaluate side-chains 356 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 277 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27032 Z= 0.240 Angle : 0.571 6.127 36860 Z= 0.304 Chirality : 0.044 0.342 4212 Planarity : 0.005 0.105 4700 Dihedral : 5.091 25.823 3856 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3396 helix: 1.38 (0.28), residues: 368 sheet: -1.36 (0.15), residues: 1124 loop : -1.55 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 89 HIS 0.008 0.001 HIS D 275 PHE 0.025 0.002 PHE G 398 TYR 0.027 0.001 TYR F 21 ARG 0.007 0.000 ARG G 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLN cc_start: 0.7303 (mp10) cc_final: 0.7096 (mp10) REVERT: D 297 LEU cc_start: 0.8055 (tp) cc_final: 0.7772 (tp) REVERT: E 221 LEU cc_start: 0.8033 (mm) cc_final: 0.7660 (mm) REVERT: F 297 LEU cc_start: 0.7747 (tp) cc_final: 0.7515 (tp) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.6497 time to fit residues: 479.1774 Evaluate side-chains 356 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.0170 chunk 292 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 HIS G 230 HIS ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27032 Z= 0.301 Angle : 0.604 6.298 36860 Z= 0.324 Chirality : 0.044 0.345 4212 Planarity : 0.005 0.057 4700 Dihedral : 5.272 27.037 3856 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.45 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3396 helix: 1.31 (0.27), residues: 368 sheet: -1.44 (0.15), residues: 1116 loop : -1.70 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 409 HIS 0.008 0.002 HIS A 230 PHE 0.030 0.002 PHE G 287 TYR 0.024 0.002 TYR F 21 ARG 0.007 0.001 ARG G 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 PHE cc_start: 0.7713 (m-80) cc_final: 0.7511 (m-80) REVERT: C 114 CYS cc_start: 0.7771 (m) cc_final: 0.7568 (t) REVERT: D 297 LEU cc_start: 0.8087 (tp) cc_final: 0.7819 (tp) REVERT: E 221 LEU cc_start: 0.7988 (mm) cc_final: 0.7675 (mm) REVERT: E 259 CYS cc_start: 0.4951 (m) cc_final: 0.4573 (m) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.6182 time to fit residues: 428.8881 Evaluate side-chains 349 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27032 Z= 0.193 Angle : 0.554 6.031 36860 Z= 0.294 Chirality : 0.045 0.344 4212 Planarity : 0.005 0.046 4700 Dihedral : 5.038 26.749 3856 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3396 helix: 1.58 (0.27), residues: 368 sheet: -1.30 (0.15), residues: 1116 loop : -1.57 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 89 HIS 0.006 0.001 HIS D 275 PHE 0.025 0.002 PHE G 398 TYR 0.019 0.001 TYR F 21 ARG 0.008 0.000 ARG H 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 CYS cc_start: 0.7786 (m) cc_final: 0.7579 (t) REVERT: D 297 LEU cc_start: 0.8013 (tp) cc_final: 0.7716 (tp) REVERT: E 221 LEU cc_start: 0.7953 (mm) cc_final: 0.7649 (mm) REVERT: E 259 CYS cc_start: 0.5106 (m) cc_final: 0.4608 (m) REVERT: F 297 LEU cc_start: 0.7783 (tp) cc_final: 0.7523 (tp) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.6438 time to fit residues: 463.7180 Evaluate side-chains 360 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27032 Z= 0.201 Angle : 0.546 6.134 36860 Z= 0.288 Chirality : 0.044 0.345 4212 Planarity : 0.005 0.048 4700 Dihedral : 4.941 25.742 3856 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3396 helix: 1.70 (0.27), residues: 368 sheet: -1.25 (0.15), residues: 1116 loop : -1.54 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 38 HIS 0.011 0.001 HIS G 392 PHE 0.022 0.002 PHE C 95 TYR 0.017 0.001 TYR F 21 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 257 PHE cc_start: 0.7370 (m-80) cc_final: 0.6243 (m-80) REVERT: A 369 LEU cc_start: 0.7085 (tt) cc_final: 0.6749 (tt) REVERT: C 114 CYS cc_start: 0.7784 (m) cc_final: 0.7553 (t) REVERT: D 297 LEU cc_start: 0.8007 (tp) cc_final: 0.7734 (tp) REVERT: D 392 ILE cc_start: 0.8402 (pt) cc_final: 0.8110 (tt) REVERT: E 221 LEU cc_start: 0.7871 (mm) cc_final: 0.7525 (mm) REVERT: F 297 LEU cc_start: 0.7795 (tp) cc_final: 0.7536 (tp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.6375 time to fit residues: 448.4089 Evaluate side-chains 358 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 301 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 27032 Z= 0.381 Angle : 0.654 7.742 36860 Z= 0.353 Chirality : 0.045 0.352 4212 Planarity : 0.005 0.065 4700 Dihedral : 5.529 28.728 3856 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3396 helix: 1.36 (0.27), residues: 368 sheet: -1.48 (0.15), residues: 1108 loop : -1.84 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 239 HIS 0.012 0.002 HIS A 230 PHE 0.028 0.002 PHE B 262 TYR 0.024 0.002 TYR F 21 ARG 0.008 0.001 ARG H 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 35 GLU cc_start: 0.7025 (pm20) cc_final: 0.6352 (mp0) REVERT: D 297 LEU cc_start: 0.8118 (tp) cc_final: 0.7835 (tp) REVERT: D 329 LEU cc_start: 0.7869 (tp) cc_final: 0.7655 (tp) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.6647 time to fit residues: 440.8126 Evaluate side-chains 331 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 9.9990 chunk 319 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 221 optimal weight: 0.9990 chunk 334 optimal weight: 6.9990 chunk 308 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 163 optimal weight: 0.0270 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27032 Z= 0.184 Angle : 0.562 6.866 36860 Z= 0.297 Chirality : 0.046 0.350 4212 Planarity : 0.005 0.047 4700 Dihedral : 5.077 26.592 3856 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3396 helix: 1.74 (0.27), residues: 368 sheet: -1.29 (0.15), residues: 1088 loop : -1.62 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 409 HIS 0.007 0.001 HIS G 392 PHE 0.043 0.002 PHE B 145 TYR 0.017 0.001 TYR H 331 ARG 0.009 0.001 ARG H 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6792 Ramachandran restraints generated. 3396 Oldfield, 0 Emsley, 3396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 114 CYS cc_start: 0.7889 (m) cc_final: 0.7415 (t) REVERT: D 297 LEU cc_start: 0.7952 (tp) cc_final: 0.7662 (tp) REVERT: D 392 ILE cc_start: 0.8483 (pt) cc_final: 0.8253 (tt) REVERT: E 221 LEU cc_start: 0.7819 (mm) cc_final: 0.7505 (mm) REVERT: F 297 LEU cc_start: 0.7877 (tp) cc_final: 0.7626 (tp) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.7102 time to fit residues: 505.1599 Evaluate side-chains 355 residues out of total 2892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 266 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 274 optimal weight: 0.0670 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081531 restraints weight = 306982.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084845 restraints weight = 126727.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.086857 restraints weight = 68387.200| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27032 Z= 0.320 Angle : 0.613 6.233 36860 Z= 0.329 Chirality : 0.044 0.350 4212 Planarity : 0.005 0.048 4700 Dihedral : 5.323 28.004 3856 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.78 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3396 helix: 1.64 (0.27), residues: 368 sheet: -1.44 (0.15), residues: 1100 loop : -1.76 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 409 HIS 0.010 0.002 HIS A 230 PHE 0.025 0.002 PHE B 262 TYR 0.020 0.002 TYR G 308 ARG 0.008 0.001 ARG C 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9302.18 seconds wall clock time: 162 minutes 44.85 seconds (9764.85 seconds total)