Starting phenix.real_space_refine on Sat Aug 23 23:17:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0c_36760/08_2025/8k0c_36760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0c_36760/08_2025/8k0c_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_36760/08_2025/8k0c_36760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0c_36760/08_2025/8k0c_36760.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0c_36760/08_2025/8k0c_36760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0c_36760/08_2025/8k0c_36760.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: G, H, B, D Time building chain proxies: 4.80, per 1000 atoms: 0.31 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=26, 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 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.02 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS D 146 " distance=2.01 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 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: 1.23 Conformation dependent library (CDL) restraints added in 686.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.84 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: 3.10 Time building geometry restraints manager: 1.65 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: 8980 14.83 - 29.66: 334 29.66 - 44.49: 92 44.49 - 59.32: 16 59.32 - 74.15: 6 Dihedral angle restraints: 9428 sinusoidal: 3682 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=" CB CYS B 146 " pdb=" SG CYS B 146 " pdb=" SG CYS D 146 " pdb=" CB CYS D 146 " ideal model delta sinusoidal sigma weight residual 93.00 161.19 -68.19 1 1.00e+01 1.00e-02 6.03e+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 ... (remaining 9425 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: 2.25 - 2.78: 3037 2.78 - 3.31: 13294 3.31 - 3.84: 26447 3.84 - 4.37: 30150 4.37 - 4.90: 53579 Nonbonded interactions: 126507 Sorted by model distance: nonbonded pdb=" OG SER A 298 " pdb=" O GLY A 301 " model vdw 2.248 3.040 nonbonded pdb=" OG SER B 298 " pdb=" O GLY B 301 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR B 135 " pdb=" OG SER D 134 " model vdw 2.258 3.040 nonbonded pdb=" O ALA A 223 " pdb=" OH TYR A 291 " model vdw 2.267 3.040 nonbonded pdb=" O ALA B 223 " pdb=" OH TYR B 291 " model vdw 2.267 3.040 ... (remaining 126502 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: 0.03 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 9.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- 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 15646 Z= 0.340 Angle : 0.905 9.995 21322 Z= 0.488 Chirality : 0.056 0.213 2418 Planarity : 0.008 0.070 2724 Dihedral : 8.924 74.149 5670 Min Nonbonded Distance : 2.248 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 495 TYR 0.053 0.003 TYR B 351 PHE 0.024 0.004 PHE A 466 TRP 0.031 0.003 TRP G 119 HIS 0.005 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00819 (15620) covalent geometry : angle 0.90394 (21270) SS BOND : bond 0.00735 ( 26) SS BOND : angle 1.35099 ( 52) hydrogen bonds : bond 0.23534 ( 552) hydrogen bonds : angle 10.26312 ( 1686) *********************** 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 : 0.641 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: 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: 0.5032 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1568 time to fit residues: 64.2664 Evaluate side-chains 155 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 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 E 187 GLN F 90 GLN F 123 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.092337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062073 restraints weight = 48931.887| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.18 r_work: 0.3124 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15646 Z= 0.164 Angle : 0.657 8.728 21322 Z= 0.346 Chirality : 0.047 0.184 2418 Planarity : 0.006 0.059 2724 Dihedral : 5.688 45.479 2124 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.43 % Allowed : 6.34 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.18), residues: 1966 helix: -0.28 (0.34), residues: 232 sheet: -1.89 (0.18), residues: 722 loop : -1.88 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 495 TYR 0.020 0.002 TYR B 351 PHE 0.017 0.002 PHE C 148 TRP 0.013 0.001 TRP G 119 HIS 0.002 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00363 (15620) covalent geometry : angle 0.65226 (21270) SS BOND : bond 0.00263 ( 26) SS BOND : angle 1.74915 ( 52) hydrogen bonds : bond 0.04350 ( 552) hydrogen bonds : angle 6.85044 ( 1686) *********************** 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 203 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.666 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: E 51 TYR cc_start: 0.8870 (p90) cc_final: 0.8653 (p90) REVERT: F 4 MET cc_start: 0.8516 (mmm) cc_final: 0.8289 (mmp) REVERT: F 90 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8801 (pp30) REVERT: A 130 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8831 (mptt) REVERT: A 228 TYR cc_start: 0.8885 (m-80) cc_final: 0.8640 (m-80) REVERT: A 333 HIS cc_start: 0.8527 (t70) cc_final: 0.8155 (t70) REVERT: C 104 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8641 (mm-30) REVERT: C 139 ASN cc_start: 0.8851 (m-40) cc_final: 0.8632 (t0) REVERT: G 51 TYR cc_start: 0.8864 (p90) cc_final: 0.8645 (p90) REVERT: H 4 MET cc_start: 0.8518 (mmm) cc_final: 0.8290 (mmp) REVERT: H 90 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8795 (pp30) REVERT: B 130 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8829 (mptt) REVERT: B 228 TYR cc_start: 0.8888 (m-80) cc_final: 0.8638 (m-80) REVERT: B 333 HIS cc_start: 0.8533 (t70) cc_final: 0.8160 (t70) REVERT: D 139 ASN cc_start: 0.8888 (m-40) cc_final: 0.8662 (t0) outliers start: 25 outliers final: 7 residues processed: 188 average time/residue: 0.1417 time to fit residues: 38.8075 Evaluate side-chains 154 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 GLN 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 H residue 90 GLN Chi-restraints excluded: chain B residue 216 CYS 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 130 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 174 optimal weight: 0.0870 chunk 182 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 159 GLN A 381 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN H 159 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.091310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060907 restraints weight = 49454.719| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.05 r_work: 0.3088 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15646 Z= 0.189 Angle : 0.613 7.434 21322 Z= 0.319 Chirality : 0.046 0.157 2418 Planarity : 0.005 0.056 2724 Dihedral : 5.286 44.129 2124 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.20 % Allowed : 7.20 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.18), residues: 1966 helix: 0.23 (0.35), residues: 234 sheet: -1.67 (0.18), residues: 728 loop : -1.68 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 210 TYR 0.018 0.002 TYR H 92 PHE 0.014 0.002 PHE C 148 TRP 0.013 0.001 TRP G 119 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00429 (15620) covalent geometry : angle 0.60841 (21270) SS BOND : bond 0.00282 ( 26) SS BOND : angle 1.64085 ( 52) hydrogen bonds : bond 0.03818 ( 552) hydrogen bonds : angle 6.17642 ( 1686) *********************** 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 171 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.686 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 51 TYR cc_start: 0.8950 (p90) cc_final: 0.8651 (p90) REVERT: F 168 LYS cc_start: 0.9049 (mttt) cc_final: 0.8824 (pptt) REVERT: A 228 TYR cc_start: 0.8893 (m-80) cc_final: 0.8612 (m-80) REVERT: A 333 HIS cc_start: 0.8535 (t70) cc_final: 0.8126 (t70) REVERT: G 51 TYR cc_start: 0.8945 (p90) cc_final: 0.8652 (p90) REVERT: H 168 LYS cc_start: 0.9048 (mttt) cc_final: 0.8824 (pptt) REVERT: B 228 TYR cc_start: 0.8889 (m-80) cc_final: 0.8599 (m-80) REVERT: B 333 HIS cc_start: 0.8527 (t70) cc_final: 0.8120 (t70) outliers start: 21 outliers final: 10 residues processed: 161 average time/residue: 0.1507 time to fit residues: 35.0546 Evaluate side-chains 137 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 H residue 194 GLU 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 188 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 140 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 492 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 492 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.089303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058258 restraints weight = 49723.334| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.09 r_work: 0.3044 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 15646 Z= 0.270 Angle : 0.642 6.762 21322 Z= 0.334 Chirality : 0.047 0.174 2418 Planarity : 0.005 0.054 2724 Dihedral : 5.260 45.619 2124 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.71 % Allowed : 8.80 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.18), residues: 1966 helix: 0.95 (0.36), residues: 222 sheet: -1.57 (0.18), residues: 734 loop : -1.44 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 210 TYR 0.016 0.002 TYR B 351 PHE 0.018 0.002 PHE A 148 TRP 0.012 0.002 TRP E 119 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00616 (15620) covalent geometry : angle 0.63874 (21270) SS BOND : bond 0.00329 ( 26) SS BOND : angle 1.46330 ( 52) hydrogen bonds : bond 0.03761 ( 552) hydrogen bonds : angle 6.05291 ( 1686) *********************** 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 163 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.506 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 51 TYR cc_start: 0.9008 (p90) cc_final: 0.8656 (p90) REVERT: E 100 ASP cc_start: 0.9374 (t70) cc_final: 0.9070 (m-30) REVERT: A 113 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: A 455 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: C 145 LYS cc_start: 0.9252 (mmmt) cc_final: 0.9041 (mmmt) REVERT: G 51 TYR cc_start: 0.9006 (p90) cc_final: 0.8640 (p90) REVERT: G 100 ASP cc_start: 0.9365 (t70) cc_final: 0.9060 (m-30) REVERT: B 113 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: B 455 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7923 (tt0) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 0.1250 time to fit residues: 28.7165 Evaluate side-chains 141 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 125 LYS Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 256 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 455 GLN Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 256 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 118 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 177 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.091339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060639 restraints weight = 49035.177| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 4.08 r_work: 0.3082 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15646 Z= 0.128 Angle : 0.564 6.693 21322 Z= 0.294 Chirality : 0.046 0.147 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.951 42.514 2124 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.89 % Allowed : 8.97 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.19), residues: 1966 helix: 1.25 (0.35), residues: 222 sheet: -1.35 (0.18), residues: 746 loop : -1.20 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 210 TYR 0.015 0.001 TYR E 51 PHE 0.022 0.002 PHE F 115 TRP 0.009 0.001 TRP E 119 HIS 0.003 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00287 (15620) covalent geometry : angle 0.56176 (21270) SS BOND : bond 0.00181 ( 26) SS BOND : angle 1.08712 ( 52) hydrogen bonds : bond 0.03246 ( 552) hydrogen bonds : angle 5.75457 ( 1686) *********************** 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 172 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.525 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 51 TYR cc_start: 0.8903 (p90) cc_final: 0.8558 (p90) REVERT: A 333 HIS cc_start: 0.8515 (t70) cc_final: 0.8175 (t70) REVERT: A 455 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: C 145 LYS cc_start: 0.9233 (mmmt) cc_final: 0.9031 (mmmt) REVERT: G 51 TYR cc_start: 0.8904 (p90) cc_final: 0.8540 (p90) REVERT: B 113 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: B 333 HIS cc_start: 0.8501 (t70) cc_final: 0.8162 (t70) REVERT: B 455 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7796 (tt0) outliers start: 33 outliers final: 21 residues processed: 163 average time/residue: 0.1185 time to fit residues: 29.3398 Evaluate side-chains 132 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 125 LYS 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 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 C residue 109 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 125 LYS Chi-restraints excluded: chain H residue 194 GLU Chi-restraints excluded: chain B residue 113 ASP 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 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 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 59 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 195 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.0010 chunk 188 optimal weight: 3.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.091222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060623 restraints weight = 48706.589| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.17 r_work: 0.3081 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15646 Z= 0.135 Angle : 0.573 7.607 21322 Z= 0.295 Chirality : 0.046 0.221 2418 Planarity : 0.004 0.051 2724 Dihedral : 4.789 39.638 2124 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.60 % Allowed : 9.49 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.19), residues: 1966 helix: 1.31 (0.36), residues: 222 sheet: -1.25 (0.18), residues: 756 loop : -1.08 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 210 TYR 0.013 0.001 TYR E 51 PHE 0.015 0.002 PHE F 115 TRP 0.008 0.001 TRP E 119 HIS 0.003 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00306 (15620) covalent geometry : angle 0.57215 (21270) SS BOND : bond 0.00207 ( 26) SS BOND : angle 0.95641 ( 52) hydrogen bonds : bond 0.03186 ( 552) hydrogen bonds : angle 5.64283 ( 1686) *********************** 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 156 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 TYR cc_start: 0.8892 (p90) cc_final: 0.8550 (p90) REVERT: A 113 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 333 HIS cc_start: 0.8497 (t70) cc_final: 0.8163 (t70) REVERT: A 455 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: C 145 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8997 (mmmt) REVERT: G 51 TYR cc_start: 0.8879 (p90) cc_final: 0.8516 (p90) REVERT: B 333 HIS cc_start: 0.8498 (t70) cc_final: 0.8158 (t70) REVERT: B 455 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7734 (tt0) outliers start: 28 outliers final: 18 residues processed: 148 average time/residue: 0.1293 time to fit residues: 28.8378 Evaluate side-chains 130 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 181 LEU 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 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 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 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 0.0050 chunk 44 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.090809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060145 restraints weight = 48777.701| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.10 r_work: 0.3069 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15646 Z= 0.154 Angle : 0.573 6.599 21322 Z= 0.296 Chirality : 0.045 0.172 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.757 38.177 2124 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.43 % Allowed : 10.23 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.19), residues: 1966 helix: 1.50 (0.36), residues: 222 sheet: -1.14 (0.19), residues: 756 loop : -0.99 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 210 TYR 0.013 0.001 TYR G 51 PHE 0.018 0.001 PHE H 115 TRP 0.010 0.001 TRP E 119 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00350 (15620) covalent geometry : angle 0.57226 (21270) SS BOND : bond 0.00218 ( 26) SS BOND : angle 0.90129 ( 52) hydrogen bonds : bond 0.03173 ( 552) hydrogen bonds : angle 5.52981 ( 1686) *********************** 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 149 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.625 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 51 TYR cc_start: 0.8895 (p90) cc_final: 0.8526 (p90) REVERT: A 333 HIS cc_start: 0.8555 (t70) cc_final: 0.8186 (t70) REVERT: A 399 MET cc_start: 0.8936 (mmt) cc_final: 0.8339 (mmt) REVERT: A 455 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: C 145 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8974 (mmmt) REVERT: G 51 TYR cc_start: 0.8892 (p90) cc_final: 0.8510 (p90) REVERT: B 333 HIS cc_start: 0.8544 (t70) cc_final: 0.8176 (t70) REVERT: B 399 MET cc_start: 0.8931 (mmt) cc_final: 0.8341 (mmt) REVERT: B 455 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7744 (tt0) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.1175 time to fit residues: 25.5622 Evaluate side-chains 131 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 0.0370 chunk 141 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.090631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059932 restraints weight = 49323.918| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 4.13 r_work: 0.3063 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15646 Z= 0.156 Angle : 0.573 8.136 21322 Z= 0.294 Chirality : 0.045 0.176 2418 Planarity : 0.004 0.051 2724 Dihedral : 4.693 36.378 2124 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.49 % Allowed : 10.23 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.19), residues: 1966 helix: 1.43 (0.36), residues: 224 sheet: -1.10 (0.19), residues: 760 loop : -0.91 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 487 TYR 0.013 0.001 TYR E 51 PHE 0.016 0.001 PHE H 115 TRP 0.009 0.001 TRP E 119 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00352 (15620) covalent geometry : angle 0.57137 (21270) SS BOND : bond 0.00208 ( 26) SS BOND : angle 0.94288 ( 52) hydrogen bonds : bond 0.03166 ( 552) hydrogen bonds : angle 5.45461 ( 1686) *********************** 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 146 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.486 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 51 TYR cc_start: 0.8867 (p90) cc_final: 0.8546 (p90) REVERT: A 113 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: A 318 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7505 (ttp-170) REVERT: A 333 HIS cc_start: 0.8584 (t70) cc_final: 0.8300 (t70) REVERT: A 399 MET cc_start: 0.8949 (mmt) cc_final: 0.8447 (mmt) REVERT: A 455 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: C 145 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8960 (mmmt) REVERT: G 51 TYR cc_start: 0.8882 (p90) cc_final: 0.8545 (p90) REVERT: B 318 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7504 (ttp-170) REVERT: B 333 HIS cc_start: 0.8567 (t70) cc_final: 0.8284 (t70) REVERT: B 399 MET cc_start: 0.8941 (mmt) cc_final: 0.8304 (mmt) REVERT: B 455 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7742 (tt0) outliers start: 26 outliers final: 21 residues processed: 141 average time/residue: 0.1198 time to fit residues: 25.6582 Evaluate side-chains 138 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain A residue 113 ASP 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 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 181 LEU Chi-restraints excluded: chain B residue 256 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 471 THR Chi-restraints excluded: chain D residue 99 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 5 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.090058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059206 restraints weight = 49201.229| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 4.08 r_work: 0.3046 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15646 Z= 0.182 Angle : 0.592 9.426 21322 Z= 0.303 Chirality : 0.046 0.193 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.708 35.995 2124 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.54 % Allowed : 10.46 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1966 helix: 1.49 (0.36), residues: 224 sheet: -1.02 (0.19), residues: 740 loop : -0.84 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 487 TYR 0.013 0.001 TYR E 51 PHE 0.018 0.002 PHE H 115 TRP 0.011 0.001 TRP E 119 HIS 0.005 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00414 (15620) covalent geometry : angle 0.59137 (21270) SS BOND : bond 0.00238 ( 26) SS BOND : angle 0.90976 ( 52) hydrogen bonds : bond 0.03218 ( 552) hydrogen bonds : angle 5.43938 ( 1686) *********************** 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 144 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 TYR cc_start: 0.8906 (p90) cc_final: 0.8515 (p90) REVERT: A 318 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7756 (ptm160) REVERT: A 333 HIS cc_start: 0.8583 (t70) cc_final: 0.8005 (t70) REVERT: A 399 MET cc_start: 0.9013 (mmt) cc_final: 0.8552 (mmt) REVERT: A 455 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: C 145 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8956 (mmmt) REVERT: G 51 TYR cc_start: 0.8903 (p90) cc_final: 0.8502 (p90) REVERT: B 318 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7751 (ptm160) REVERT: B 333 HIS cc_start: 0.8574 (t70) cc_final: 0.8000 (t70) REVERT: B 399 MET cc_start: 0.9005 (mmt) cc_final: 0.8388 (mmt) REVERT: B 455 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: D 144 GLU cc_start: 0.8475 (tt0) cc_final: 0.8260 (tt0) outliers start: 27 outliers final: 19 residues processed: 138 average time/residue: 0.1145 time to fit residues: 24.2371 Evaluate side-chains 133 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain A residue 256 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 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 256 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 471 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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** ** B 509 ASN ** 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 = 0.3951 r_free = 0.3951 target = 0.090866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.060171 restraints weight = 48839.178| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.10 r_work: 0.3068 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15646 Z= 0.139 Angle : 0.581 9.662 21322 Z= 0.296 Chirality : 0.046 0.269 2418 Planarity : 0.004 0.048 2724 Dihedral : 4.649 34.020 2124 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.20 % Allowed : 10.91 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.20), residues: 1966 helix: 1.49 (0.36), residues: 224 sheet: -1.02 (0.19), residues: 752 loop : -0.72 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.013 0.001 TYR G 51 PHE 0.018 0.001 PHE F 115 TRP 0.010 0.001 TRP G 35 HIS 0.004 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00314 (15620) covalent geometry : angle 0.58049 (21270) SS BOND : bond 0.00193 ( 26) SS BOND : angle 0.84169 ( 52) hydrogen bonds : bond 0.03136 ( 552) hydrogen bonds : angle 5.37765 ( 1686) ********************** 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 138 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 TYR cc_start: 0.8846 (p90) cc_final: 0.8635 (p90) REVERT: A 318 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7578 (ttp-170) REVERT: A 333 HIS cc_start: 0.8549 (t70) cc_final: 0.8269 (t70) REVERT: A 399 MET cc_start: 0.9000 (mmt) cc_final: 0.8557 (mmt) REVERT: A 455 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: C 145 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8956 (mmmt) REVERT: G 51 TYR cc_start: 0.8852 (p90) cc_final: 0.8624 (p90) REVERT: B 318 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7524 (ttp-170) REVERT: B 333 HIS cc_start: 0.8543 (t70) cc_final: 0.8267 (t70) REVERT: B 399 MET cc_start: 0.9001 (mmt) cc_final: 0.8553 (mmt) REVERT: B 455 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7717 (tt0) outliers start: 21 outliers final: 17 residues processed: 133 average time/residue: 0.1153 time to fit residues: 23.6172 Evaluate side-chains 134 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain A residue 256 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 471 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 256 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 471 THR Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.089522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058718 restraints weight = 49213.204| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.01 r_work: 0.3062 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15646 Z= 0.206 Angle : 0.605 9.338 21322 Z= 0.308 Chirality : 0.046 0.207 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.717 34.887 2124 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.26 % Allowed : 10.97 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.20), residues: 1966 helix: 1.46 (0.36), residues: 226 sheet: -1.04 (0.19), residues: 754 loop : -0.79 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 338 TYR 0.013 0.002 TYR E 51 PHE 0.017 0.002 PHE H 115 TRP 0.010 0.001 TRP E 119 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00468 (15620) covalent geometry : angle 0.60384 (21270) SS BOND : bond 0.00267 ( 26) SS BOND : angle 0.90370 ( 52) hydrogen bonds : bond 0.03305 ( 552) hydrogen bonds : angle 5.42507 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.25 seconds wall clock time: 80 minutes 43.49 seconds (4843.49 seconds total)