Starting phenix.real_space_refine on Tue Dec 31 09:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0c_36760/12_2024/8k0c_36760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0c_36760/12_2024/8k0c_36760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0c_36760/12_2024/8k0c_36760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0c_36760/12_2024/8k0c_36760.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0c_36760/12_2024/8k0c_36760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0c_36760/12_2024/8k0c_36760.cif" } resolution = 3.18 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9656 2.51 5 N 2550 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15262 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3749 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 450} Chain breaks: 1 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 420 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Restraints were copied for chains: H, G, D, B Time building chain proxies: 12.31, per 1000 atoms: 0.81 Number of scatterers: 15262 At special positions: 0 Unit cell: (168.1, 84.46, 174.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2986 8.00 N 2550 7.00 C 9656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.02 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 14.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 118 through 146 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.815A pdb=" N GLN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.763A pdb=" N LEU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 118 through 146 removed outlier: 3.554A pdb=" N ALA C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'H' and resid 120 through 127 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 118 through 146 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.815A pdb=" N GLN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.763A pdb=" N LEU B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.554A pdb=" N ALA D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.860A pdb=" N VAL E 12 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.559A pdb=" N ALA E 98 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 118 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR E 101 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE E 116 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR E 103 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASN E 114 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AA6, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AA7, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.593A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.687A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 153 through 154 removed outlier: 4.580A pdb=" N TRP F 147 " --> pdb=" O GLN F 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 579 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 579 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 217 through 222 removed outlier: 5.880A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 279 through 286 removed outlier: 5.602A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 313 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 347 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 356 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.562A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 468 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.555A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU G 82 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU G 82 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.860A pdb=" N VAL G 12 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 47 through 48 removed outlier: 3.559A pdb=" N ALA G 98 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL G 118 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR G 101 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE G 116 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR G 103 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASN G 114 " --> pdb=" O TYR G 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC8, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC9, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AD1, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER H 7 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.593A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 113 through 117 removed outlier: 3.687A pdb=" N ASN H 136 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR H 172 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 154 removed outlier: 4.580A pdb=" N TRP H 147 " --> pdb=" O GLN H 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 579 " --> pdb=" O LYS B 560 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 579 " --> pdb=" O LYS B 560 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 217 through 222 removed outlier: 5.880A pdb=" N SER B 232 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 222 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA B 230 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 279 through 286 removed outlier: 5.602A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 313 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 356 " --> pdb=" O TYR B 363 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.562A pdb=" N SER B 447 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.555A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1686 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: 6.58 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4802 1.34 - 1.46: 3438 1.46 - 1.58: 7292 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 15620 Sorted by residual: bond pdb=" CD LYS A 465 " pdb=" CE LYS A 465 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CD LYS B 465 " pdb=" CE LYS B 465 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CB TYR B 291 " pdb=" CG TYR B 291 " ideal model delta sigma weight residual 1.512 1.468 0.044 2.20e-02 2.07e+03 4.05e+00 bond pdb=" CB TYR A 291 " pdb=" CG TYR A 291 " ideal model delta sigma weight residual 1.512 1.468 0.044 2.20e-02 2.07e+03 4.05e+00 bond pdb=" C SER B 486 " pdb=" N ARG B 487 " ideal model delta sigma weight residual 1.331 1.301 0.030 1.59e-02 3.96e+03 3.49e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 20387 2.00 - 4.00: 763 4.00 - 6.00: 84 6.00 - 8.00: 30 8.00 - 9.99: 6 Bond angle restraints: 21270 Sorted by residual: angle pdb=" C THR F 50 " pdb=" N ALA F 51 " pdb=" CA ALA F 51 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C THR H 50 " pdb=" N ALA H 51 " pdb=" CA ALA H 51 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C THR F 94 " pdb=" N PRO F 95 " pdb=" CA PRO F 95 " ideal model delta sigma weight residual 127.00 134.92 -7.92 2.40e+00 1.74e-01 1.09e+01 angle pdb=" C THR H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 127.00 134.92 -7.92 2.40e+00 1.74e-01 1.09e+01 angle pdb=" N LYS E 217 " pdb=" CA LYS E 217 " pdb=" C LYS E 217 " ideal model delta sigma weight residual 109.81 116.76 -6.95 2.21e+00 2.05e-01 9.89e+00 ... (remaining 21265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.83: 8967 14.83 - 29.66: 320 29.66 - 44.49: 84 44.49 - 59.32: 13 59.32 - 74.15: 5 Dihedral angle restraints: 9389 sinusoidal: 3643 harmonic: 5746 Sorted by residual: dihedral pdb=" CB CYS A 146 " pdb=" SG CYS A 146 " pdb=" SG CYS C 146 " pdb=" CB CYS C 146 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CA GLY G 107 " pdb=" C GLY G 107 " pdb=" N SER G 108 " pdb=" CA SER G 108 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY E 107 " pdb=" C GLY E 107 " pdb=" N SER E 108 " pdb=" CA SER E 108 " ideal model delta harmonic sigma weight residual 180.00 150.80 29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 9386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1471 0.043 - 0.085: 605 0.085 - 0.128: 274 0.128 - 0.171: 56 0.171 - 0.213: 12 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CB THR A 531 " pdb=" CA THR A 531 " pdb=" OG1 THR A 531 " pdb=" CG2 THR A 531 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB THR B 531 " pdb=" CA THR B 531 " pdb=" OG1 THR B 531 " pdb=" CG2 THR B 531 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE B 444 " pdb=" CA ILE B 444 " pdb=" CG1 ILE B 444 " pdb=" CG2 ILE B 444 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2415 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 351 " 0.026 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" CG TYR B 351 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B 351 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 351 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 351 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 351 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 351 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " -0.026 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" CG TYR A 351 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU G 164 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO G 165 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 165 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 165 " -0.034 5.00e-02 4.00e+02 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 133 2.59 - 3.16: 11934 3.16 - 3.74: 23739 3.74 - 4.32: 33792 4.32 - 4.90: 56948 Nonbonded interactions: 126546 Sorted by model distance: nonbonded pdb=" SG CYS B 146 " pdb=" SG CYS D 146 " model vdw 2.007 3.760 nonbonded pdb=" SG CYS B 565 " pdb=" SG CYS B 574 " model vdw 2.019 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS B 387 " pdb=" SG CYS B 499 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS B 382 " pdb=" SG CYS B 395 " model vdw 2.027 3.760 ... (remaining 126541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.940 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: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 40.490 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.008 0.082 15620 Z= 0.539 Angle : 0.904 9.995 21270 Z= 0.488 Chirality : 0.056 0.213 2418 Planarity : 0.008 0.070 2724 Dihedral : 8.924 74.149 5670 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -3.42 (0.17), residues: 1966 helix: -1.98 (0.26), residues: 232 sheet: -2.29 (0.18), residues: 686 loop : -2.30 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 119 HIS 0.005 0.001 HIS B 281 PHE 0.024 0.004 PHE A 466 TYR 0.053 0.003 TYR B 351 ARG 0.008 0.001 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.814 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: E 160 ASP cc_start: 0.9123 (m-30) cc_final: 0.8298 (p0) REVERT: F 115 PHE cc_start: 0.5608 (m-80) cc_final: 0.5036 (m-80) REVERT: G 160 ASP cc_start: 0.9124 (m-30) cc_final: 0.8297 (p0) REVERT: H 115 PHE cc_start: 0.5606 (m-80) cc_final: 0.5033 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3328 time to fit residues: 135.6682 Evaluate side-chains 153 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN F 90 GLN F 123 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 233 HIS A 358 GLN A 423 ASN C 141 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN H 90 GLN H 123 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 233 HIS B 358 GLN B 423 ASN D 141 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15620 Z= 0.258 Angle : 0.656 8.735 21270 Z= 0.345 Chirality : 0.047 0.203 2418 Planarity : 0.006 0.059 2724 Dihedral : 5.629 45.829 2124 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.14 % Allowed : 6.74 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -2.60 (0.18), residues: 1966 helix: -0.26 (0.34), residues: 232 sheet: -1.91 (0.18), residues: 722 loop : -1.87 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 119 HIS 0.004 0.001 HIS B 281 PHE 0.018 0.002 PHE D 148 TYR 0.020 0.002 TYR G 51 ARG 0.007 0.001 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 1.878 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: E 160 ASP cc_start: 0.9039 (m-30) cc_final: 0.8388 (p0) REVERT: F 4 MET cc_start: 0.8612 (mmm) cc_final: 0.8375 (mmp) REVERT: G 160 ASP cc_start: 0.9034 (m-30) cc_final: 0.8381 (p0) outliers start: 20 outliers final: 6 residues processed: 183 average time/residue: 0.3143 time to fit residues: 83.7193 Evaluate side-chains 139 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN F 159 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 492 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 492 GLN ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15620 Z= 0.216 Angle : 0.599 11.973 21270 Z= 0.311 Chirality : 0.046 0.160 2418 Planarity : 0.005 0.055 2724 Dihedral : 5.179 43.426 2124 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.09 % Allowed : 7.71 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 1966 helix: 0.20 (0.35), residues: 232 sheet: -1.66 (0.18), residues: 732 loop : -1.69 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 119 HIS 0.006 0.001 HIS E 113 PHE 0.019 0.002 PHE C 148 TYR 0.025 0.002 TYR E 51 ARG 0.004 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.844 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: E 160 ASP cc_start: 0.9016 (m-30) cc_final: 0.8349 (p0) REVERT: F 92 TYR cc_start: 0.7850 (t80) cc_final: 0.7435 (t80) REVERT: C 139 ASN cc_start: 0.7796 (m-40) cc_final: 0.7591 (t0) REVERT: G 160 ASP cc_start: 0.9014 (m-30) cc_final: 0.8343 (p0) outliers start: 19 outliers final: 11 residues processed: 160 average time/residue: 0.3625 time to fit residues: 85.1172 Evaluate side-chains 132 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15620 Z= 0.312 Angle : 0.601 7.744 21270 Z= 0.312 Chirality : 0.046 0.166 2418 Planarity : 0.005 0.053 2724 Dihedral : 5.034 42.900 2124 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.54 % Allowed : 8.80 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.87 (0.18), residues: 1966 helix: 0.53 (0.35), residues: 234 sheet: -1.47 (0.18), residues: 730 loop : -1.42 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.007 0.001 HIS E 113 PHE 0.016 0.002 PHE A 148 TYR 0.041 0.002 TYR G 51 ARG 0.006 0.001 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.960 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: E 160 ASP cc_start: 0.9044 (m-30) cc_final: 0.8369 (p0) REVERT: F 194 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: A 455 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: G 160 ASP cc_start: 0.9046 (m-30) cc_final: 0.8373 (p0) REVERT: B 455 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7361 (tm-30) outliers start: 27 outliers final: 14 residues processed: 144 average time/residue: 0.3145 time to fit residues: 66.5051 Evaluate side-chains 129 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15620 Z= 0.321 Angle : 0.596 6.919 21270 Z= 0.310 Chirality : 0.046 0.151 2418 Planarity : 0.005 0.052 2724 Dihedral : 4.967 43.022 2124 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.17 % Allowed : 9.09 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.67 (0.19), residues: 1966 helix: 1.14 (0.36), residues: 222 sheet: -1.55 (0.18), residues: 764 loop : -1.16 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.007 0.001 HIS E 113 PHE 0.042 0.002 PHE A 148 TYR 0.039 0.002 TYR E 51 ARG 0.004 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9059 (m-30) cc_final: 0.8455 (p0) REVERT: F 18 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8174 (tpp80) REVERT: F 194 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7463 (pp20) REVERT: A 318 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7198 (ttp-170) REVERT: A 455 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: G 160 ASP cc_start: 0.9060 (m-30) cc_final: 0.8457 (p0) REVERT: H 18 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8180 (tpp80) REVERT: B 318 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7190 (ttp-170) REVERT: B 455 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7355 (tt0) outliers start: 38 outliers final: 21 residues processed: 152 average time/residue: 0.2994 time to fit residues: 67.3759 Evaluate side-chains 135 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 0.4980 chunk 37 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 GLN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15620 Z= 0.323 Angle : 0.598 6.991 21270 Z= 0.311 Chirality : 0.046 0.161 2418 Planarity : 0.005 0.051 2724 Dihedral : 4.900 42.962 2124 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.66 % Allowed : 9.83 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.51 (0.19), residues: 1966 helix: 1.13 (0.35), residues: 224 sheet: -1.38 (0.18), residues: 756 loop : -1.09 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.004 0.001 HIS G 113 PHE 0.023 0.002 PHE H 115 TYR 0.027 0.002 TYR E 51 ARG 0.004 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9056 (m-30) cc_final: 0.8493 (p0) REVERT: F 18 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8170 (tpp80) REVERT: F 194 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7547 (pp20) REVERT: A 318 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7294 (ttp-170) REVERT: A 455 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: G 160 ASP cc_start: 0.9071 (m-30) cc_final: 0.8485 (p0) REVERT: H 18 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8166 (tpp80) REVERT: B 455 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7332 (tt0) outliers start: 29 outliers final: 24 residues processed: 142 average time/residue: 0.2748 time to fit residues: 59.4892 Evaluate side-chains 127 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 118 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15620 Z= 0.229 Angle : 0.566 6.295 21270 Z= 0.293 Chirality : 0.045 0.151 2418 Planarity : 0.004 0.051 2724 Dihedral : 4.739 40.543 2124 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.77 % Allowed : 10.17 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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 (0.19), residues: 1966 helix: 1.47 (0.36), residues: 220 sheet: -1.31 (0.18), residues: 756 loop : -1.02 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 119 HIS 0.004 0.001 HIS B 333 PHE 0.018 0.001 PHE F 115 TYR 0.024 0.001 TYR G 51 ARG 0.004 0.000 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.936 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: E 160 ASP cc_start: 0.9039 (m-30) cc_final: 0.8474 (p0) REVERT: F 18 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8174 (tpp80) REVERT: F 194 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7524 (pp20) REVERT: A 399 MET cc_start: 0.8779 (mmt) cc_final: 0.8379 (mmt) REVERT: A 455 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: G 160 ASP cc_start: 0.9037 (m-30) cc_final: 0.8466 (p0) REVERT: H 18 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8176 (tpp80) REVERT: B 399 MET cc_start: 0.8808 (mmt) cc_final: 0.8393 (mmt) REVERT: B 455 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7197 (tt0) outliers start: 31 outliers final: 23 residues processed: 149 average time/residue: 0.3049 time to fit residues: 68.3223 Evaluate side-chains 128 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 148 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15620 Z= 0.378 Angle : 0.635 9.772 21270 Z= 0.325 Chirality : 0.046 0.148 2418 Planarity : 0.005 0.052 2724 Dihedral : 4.852 41.697 2124 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.89 % Allowed : 11.03 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.31 (0.19), residues: 1966 helix: 1.22 (0.36), residues: 222 sheet: -1.17 (0.19), residues: 742 loop : -1.02 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 119 HIS 0.006 0.001 HIS E 113 PHE 0.035 0.002 PHE B 148 TYR 0.025 0.002 TYR E 51 ARG 0.004 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.884 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: E 160 ASP cc_start: 0.9072 (m-30) cc_final: 0.8533 (p0) REVERT: F 18 ARG cc_start: 0.8887 (tpp80) cc_final: 0.8181 (tpp80) REVERT: F 194 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7537 (pp20) REVERT: A 399 MET cc_start: 0.8876 (mmt) cc_final: 0.8412 (mmt) REVERT: A 455 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: G 160 ASP cc_start: 0.9067 (m-30) cc_final: 0.8515 (p0) REVERT: H 18 ARG cc_start: 0.8892 (tpp80) cc_final: 0.8175 (tpp80) REVERT: B 399 MET cc_start: 0.8912 (mmt) cc_final: 0.8572 (mmt) REVERT: B 455 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7295 (tt0) outliers start: 33 outliers final: 28 residues processed: 144 average time/residue: 0.3105 time to fit residues: 68.2697 Evaluate side-chains 136 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 0.0670 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15620 Z= 0.176 Angle : 0.574 7.944 21270 Z= 0.294 Chirality : 0.045 0.176 2418 Planarity : 0.004 0.048 2724 Dihedral : 4.651 37.687 2124 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.54 % Allowed : 11.26 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.15 (0.19), residues: 1966 helix: 1.26 (0.36), residues: 226 sheet: -1.17 (0.18), residues: 760 loop : -0.80 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 35 HIS 0.003 0.000 HIS E 113 PHE 0.027 0.001 PHE B 148 TYR 0.022 0.001 TYR E 51 ARG 0.004 0.000 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.889 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: E 160 ASP cc_start: 0.9035 (m-30) cc_final: 0.8443 (p0) REVERT: F 18 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8337 (tpp80) REVERT: F 194 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7531 (pp20) REVERT: F 210 ARG cc_start: 0.5532 (ttp80) cc_final: 0.5301 (ttm110) REVERT: A 399 MET cc_start: 0.8641 (mmt) cc_final: 0.8274 (mmt) REVERT: A 455 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: G 160 ASP cc_start: 0.9025 (m-30) cc_final: 0.8438 (p0) REVERT: H 18 ARG cc_start: 0.8833 (tpp80) cc_final: 0.8338 (tpp80) REVERT: B 399 MET cc_start: 0.8749 (mmt) cc_final: 0.8538 (mmt) REVERT: B 455 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: D 144 GLU cc_start: 0.7299 (tt0) cc_final: 0.7076 (tt0) REVERT: D 145 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8312 (mmmt) outliers start: 27 outliers final: 21 residues processed: 143 average time/residue: 0.2789 time to fit residues: 61.4050 Evaluate side-chains 138 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15620 Z= 0.367 Angle : 0.626 7.455 21270 Z= 0.321 Chirality : 0.046 0.166 2418 Planarity : 0.005 0.050 2724 Dihedral : 4.752 38.915 2124 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.54 % Allowed : 11.54 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.11 (0.19), residues: 1966 helix: 1.36 (0.36), residues: 224 sheet: -1.07 (0.19), residues: 746 loop : -0.86 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 119 HIS 0.006 0.001 HIS E 113 PHE 0.026 0.002 PHE B 148 TYR 0.061 0.002 TYR G 51 ARG 0.005 0.001 ARG G 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.853 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: E 160 ASP cc_start: 0.9068 (m-30) cc_final: 0.8513 (p0) REVERT: F 194 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: A 399 MET cc_start: 0.8827 (mmt) cc_final: 0.8335 (mmt) REVERT: A 455 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: G 160 ASP cc_start: 0.9061 (m-30) cc_final: 0.8511 (p0) REVERT: B 399 MET cc_start: 0.8891 (mmt) cc_final: 0.8544 (mmt) REVERT: B 455 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: D 145 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8453 (mmmt) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.2938 time to fit residues: 59.1159 Evaluate side-chains 131 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 146 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 5.9990 chunk 165 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 159 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.090238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059691 restraints weight = 49112.740| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.23 r_work: 0.3058 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15620 Z= 0.191 Angle : 0.578 9.366 21270 Z= 0.295 Chirality : 0.045 0.153 2418 Planarity : 0.004 0.047 2724 Dihedral : 4.639 36.101 2124 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.43 % Allowed : 11.66 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1966 helix: 1.48 (0.36), residues: 224 sheet: -1.00 (0.19), residues: 746 loop : -0.72 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.004 0.001 HIS E 113 PHE 0.022 0.001 PHE B 148 TYR 0.041 0.001 TYR G 51 ARG 0.004 0.000 ARG A 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3576.17 seconds wall clock time: 67 minutes 2.71 seconds (4022.71 seconds total)