Starting phenix.real_space_refine on Fri Jun 13 19:57:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0c_36760/06_2025/8k0c_36760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0c_36760/06_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_36760/06_2025/8k0c_36760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0c_36760/06_2025/8k0c_36760.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0c_36760/06_2025/8k0c_36760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0c_36760/06_2025/8k0c_36760.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 9656 2.51 5 N 2550 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15262 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3749 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 450} Chain breaks: 1 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 420 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Restraints were copied for chains: H, G, D, B Time building chain proxies: 13.56, per 1000 atoms: 0.89 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: 3.90 Conformation dependent library (CDL) restraints added in 2.4 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 40 sheets defined 14.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 120 through 127 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 118 through 146 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.815A pdb=" N GLN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.763A pdb=" N LEU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 118 through 146 removed outlier: 3.554A pdb=" N ALA C 122 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'H' and resid 120 through 127 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 118 through 146 Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.815A pdb=" N GLN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.763A pdb=" N LEU B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.554A pdb=" N ALA D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.860A pdb=" N VAL E 12 " --> pdb=" O THR E 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 48 removed outlier: 3.559A pdb=" N ALA E 98 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 118 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR E 101 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE E 116 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR E 103 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASN E 114 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AA6, first strand: chain 'E' and resid 136 through 140 Processing sheet with id=AA7, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AA8, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AA9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.593A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.687A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 153 through 154 removed outlier: 4.580A pdb=" N TRP F 147 " --> pdb=" O GLN F 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 579 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 579 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 217 through 222 removed outlier: 5.880A pdb=" N SER A 232 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 222 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA A 230 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 279 through 286 removed outlier: 5.602A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 313 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 347 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 356 " --> pdb=" O TYR A 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.562A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 450 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 468 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.555A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU G 82 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.523A pdb=" N LEU G 82 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.860A pdb=" N VAL G 12 " --> pdb=" O THR G 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 47 through 48 removed outlier: 3.559A pdb=" N ALA G 98 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL G 118 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR G 101 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE G 116 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR G 103 " --> pdb=" O ASN G 114 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASN G 114 " --> pdb=" O TYR G 103 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC8, first strand: chain 'G' and resid 136 through 140 Processing sheet with id=AC9, first strand: chain 'G' and resid 167 through 170 Processing sheet with id=AD1, first strand: chain 'G' and resid 185 through 186 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.503A pdb=" N SER H 7 " --> pdb=" O THR H 22 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.593A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 113 through 117 removed outlier: 3.687A pdb=" N ASN H 136 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR H 172 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 154 removed outlier: 4.580A pdb=" N TRP H 147 " --> pdb=" O GLN H 154 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 579 " --> pdb=" O LYS B 560 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.407A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 579 " --> pdb=" O LYS B 560 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 217 through 222 removed outlier: 5.880A pdb=" N SER B 232 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 222 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA B 230 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 237 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER B 245 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 279 through 286 removed outlier: 5.602A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 313 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.140A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 356 " --> pdb=" O TYR B 363 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.562A pdb=" N SER B 447 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B 450 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.555A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1686 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 4.40 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: 0.08 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 10.300 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 43.520 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.17), residues: 1966 helix: -1.98 (0.26), residues: 232 sheet: -2.29 (0.18), residues: 686 loop : -2.30 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP G 119 HIS 0.005 0.001 HIS B 281 PHE 0.024 0.004 PHE A 466 TYR 0.053 0.003 TYR B 351 ARG 0.008 0.001 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.23534 ( 552) hydrogen bonds : angle 10.26312 ( 1686) SS BOND : bond 0.00735 ( 26) SS BOND : angle 1.35099 ( 52) covalent geometry : bond 0.00819 (15620) covalent geometry : angle 0.90394 (21270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9123 (m-30) cc_final: 0.8298 (p0) REVERT: F 115 PHE cc_start: 0.5608 (m-80) cc_final: 0.5036 (m-80) REVERT: G 160 ASP cc_start: 0.9124 (m-30) cc_final: 0.8297 (p0) REVERT: H 115 PHE cc_start: 0.5606 (m-80) cc_final: 0.5033 (m-80) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3452 time to fit residues: 140.8546 Evaluate side-chains 153 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN F 90 GLN F 123 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 233 HIS A 358 GLN A 423 ASN C 141 ASN ** G 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN H 90 GLN H 123 GLN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 233 HIS B 358 GLN B 423 ASN D 141 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.092195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.061981 restraints weight = 48757.683| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 4.02 r_work: 0.3123 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15646 Z= 0.173 Angle : 0.659 9.353 21322 Z= 0.346 Chirality : 0.047 0.200 2418 Planarity : 0.006 0.059 2724 Dihedral : 5.685 45.657 2124 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.43 % Allowed : 6.69 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1966 helix: -0.31 (0.34), residues: 232 sheet: -1.90 (0.18), residues: 722 loop : -1.88 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 119 HIS 0.002 0.001 HIS A 281 PHE 0.017 0.002 PHE C 148 TYR 0.019 0.002 TYR A 351 ARG 0.006 0.001 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 552) hydrogen bonds : angle 6.88798 ( 1686) SS BOND : bond 0.00274 ( 26) SS BOND : angle 1.77314 ( 52) covalent geometry : bond 0.00386 (15620) covalent geometry : angle 0.65437 (21270) *********************** 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 199 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.919 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: E 160 ASP cc_start: 0.9545 (m-30) cc_final: 0.9087 (p0) REVERT: F 4 MET cc_start: 0.8501 (mmm) cc_final: 0.8278 (mmp) REVERT: F 90 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8791 (pp30) REVERT: A 130 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8830 (mptt) REVERT: A 228 TYR cc_start: 0.8888 (m-80) cc_final: 0.8644 (m-80) REVERT: A 333 HIS cc_start: 0.8540 (t70) cc_final: 0.8159 (t70) REVERT: C 139 ASN cc_start: 0.8852 (m-40) cc_final: 0.8628 (t0) REVERT: G 160 ASP cc_start: 0.9546 (m-30) cc_final: 0.9092 (p0) REVERT: H 4 MET cc_start: 0.8498 (mmm) cc_final: 0.8276 (mmp) REVERT: H 90 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8786 (pp30) REVERT: B 130 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8828 (mptt) REVERT: B 228 TYR cc_start: 0.8892 (m-80) cc_final: 0.8647 (m-80) REVERT: B 333 HIS cc_start: 0.8535 (t70) cc_final: 0.8155 (t70) REVERT: D 139 ASN cc_start: 0.8882 (m-40) cc_final: 0.8660 (t0) outliers start: 25 outliers final: 7 residues processed: 184 average time/residue: 0.3314 time to fit residues: 89.3527 Evaluate side-chains 143 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 182 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 158 optimal weight: 0.0170 chunk 118 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN F 159 GLN ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN A 492 GLN ** 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 492 GLN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.092056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061355 restraints weight = 48550.451| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.07 r_work: 0.3093 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2754 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= 0.183 Angle : 0.621 12.106 21322 Z= 0.322 Chirality : 0.046 0.158 2418 Planarity : 0.005 0.056 2724 Dihedral : 5.339 44.344 2124 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.14 % Allowed : 7.49 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.18), residues: 1966 helix: 0.14 (0.35), residues: 234 sheet: -1.71 (0.18), residues: 732 loop : -1.69 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 119 HIS 0.006 0.001 HIS E 113 PHE 0.019 0.002 PHE C 148 TYR 0.032 0.002 TYR E 51 ARG 0.003 0.001 ARG H 210 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 552) hydrogen bonds : angle 6.23129 ( 1686) SS BOND : bond 0.00285 ( 26) SS BOND : angle 1.70178 ( 52) covalent geometry : bond 0.00410 (15620) covalent geometry : angle 0.61592 (21270) *********************** 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 166 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9539 (m-30) cc_final: 0.9087 (p0) REVERT: F 168 LYS cc_start: 0.9045 (mttt) cc_final: 0.8829 (pptt) REVERT: A 113 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: A 228 TYR cc_start: 0.8870 (m-80) cc_final: 0.8613 (m-80) REVERT: A 333 HIS cc_start: 0.8535 (t70) cc_final: 0.8124 (t70) REVERT: G 160 ASP cc_start: 0.9539 (m-30) cc_final: 0.9088 (p0) REVERT: H 168 LYS cc_start: 0.9043 (mttt) cc_final: 0.8829 (pptt) REVERT: B 228 TYR cc_start: 0.8865 (m-80) cc_final: 0.8610 (m-80) REVERT: B 333 HIS cc_start: 0.8522 (t70) cc_final: 0.8115 (t70) outliers start: 20 outliers final: 11 residues processed: 158 average time/residue: 0.3306 time to fit residues: 76.4440 Evaluate side-chains 134 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 113 ASP 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 148 PHE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 58 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 326 ASN ** H 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.090161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058989 restraints weight = 49002.026| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.11 r_work: 0.3053 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15646 Z= 0.247 Angle : 0.634 6.629 21322 Z= 0.330 Chirality : 0.047 0.174 2418 Planarity : 0.005 0.054 2724 Dihedral : 5.255 45.126 2124 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.66 % Allowed : 8.91 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 1966 helix: 0.82 (0.35), residues: 222 sheet: -1.56 (0.18), residues: 738 loop : -1.36 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 119 HIS 0.007 0.001 HIS G 113 PHE 0.014 0.002 PHE A 364 TYR 0.040 0.002 TYR E 51 ARG 0.006 0.001 ARG H 210 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 552) hydrogen bonds : angle 5.98766 ( 1686) SS BOND : bond 0.00384 ( 26) SS BOND : angle 1.32582 ( 52) covalent geometry : bond 0.00558 (15620) covalent geometry : angle 0.63109 (21270) *********************** 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 157 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9530 (m-30) cc_final: 0.9068 (p0) REVERT: F 168 LYS cc_start: 0.9048 (mttt) cc_final: 0.8829 (pptt) REVERT: F 194 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: A 113 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: A 455 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: C 145 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8992 (mmmt) REVERT: G 160 ASP cc_start: 0.9531 (m-30) cc_final: 0.9071 (p0) REVERT: H 168 LYS cc_start: 0.9046 (mttt) cc_final: 0.8828 (pptt) REVERT: H 194 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: B 113 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: B 455 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7905 (tt0) outliers start: 29 outliers final: 15 residues processed: 148 average time/residue: 0.3020 time to fit residues: 65.6472 Evaluate side-chains 133 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain A residue 113 ASP 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 C residue 109 VAL Chi-restraints excluded: chain G residue 47 GLU 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 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 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 131 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.091633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060836 restraints weight = 49299.856| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.98 r_work: 0.3079 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3337 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= 0.145 Angle : 0.574 7.027 21322 Z= 0.299 Chirality : 0.046 0.150 2418 Planarity : 0.005 0.051 2724 Dihedral : 5.019 42.879 2124 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.94 % Allowed : 8.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1966 helix: 1.19 (0.36), residues: 222 sheet: -1.43 (0.18), residues: 758 loop : -1.18 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.004 0.001 HIS E 113 PHE 0.021 0.001 PHE H 115 TYR 0.020 0.001 TYR G 51 ARG 0.005 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 552) hydrogen bonds : angle 5.78155 ( 1686) SS BOND : bond 0.00232 ( 26) SS BOND : angle 0.96894 ( 52) covalent geometry : bond 0.00324 (15620) covalent geometry : angle 0.57226 (21270) *********************** 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 166 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 TYR cc_start: 0.9048 (p90) cc_final: 0.8499 (p90) REVERT: E 160 ASP cc_start: 0.9505 (m-30) cc_final: 0.9041 (p0) REVERT: F 18 ARG cc_start: 0.9160 (tpp80) cc_final: 0.8387 (tpp80) REVERT: A 333 HIS cc_start: 0.8521 (t70) cc_final: 0.8144 (t70) REVERT: A 455 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: G 51 TYR cc_start: 0.9049 (p90) cc_final: 0.8498 (p90) REVERT: G 160 ASP cc_start: 0.9504 (m-30) cc_final: 0.9040 (p0) REVERT: H 18 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8391 (tpp80) REVERT: B 113 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: B 228 TYR cc_start: 0.8851 (m-80) cc_final: 0.8557 (m-80) REVERT: B 333 HIS cc_start: 0.8513 (t70) cc_final: 0.8140 (t70) REVERT: B 455 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7803 (tt0) outliers start: 34 outliers final: 18 residues processed: 158 average time/residue: 0.2878 time to fit residues: 67.5770 Evaluate side-chains 129 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 129 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 72 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.088790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057770 restraints weight = 49550.615| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.05 r_work: 0.3037 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15646 Z= 0.274 Angle : 0.650 7.349 21322 Z= 0.336 Chirality : 0.047 0.161 2418 Planarity : 0.005 0.053 2724 Dihedral : 5.104 44.257 2124 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.00 % Allowed : 9.03 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1966 helix: 1.11 (0.36), residues: 222 sheet: -1.36 (0.19), residues: 742 loop : -1.12 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 119 HIS 0.005 0.001 HIS G 113 PHE 0.026 0.002 PHE B 364 TYR 0.021 0.002 TYR E 51 ARG 0.003 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 552) hydrogen bonds : angle 5.82408 ( 1686) SS BOND : bond 0.00354 ( 26) SS BOND : angle 1.07594 ( 52) covalent geometry : bond 0.00626 (15620) covalent geometry : angle 0.64872 (21270) *********************** 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 151 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9500 (m-30) cc_final: 0.9087 (p0) REVERT: F 18 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8336 (tpp80) REVERT: F 168 LYS cc_start: 0.7787 (pttt) cc_final: 0.6627 (pttt) REVERT: A 333 HIS cc_start: 0.8616 (t70) cc_final: 0.8097 (t70) REVERT: A 455 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: G 160 ASP cc_start: 0.9499 (m-30) cc_final: 0.9088 (p0) REVERT: H 18 ARG cc_start: 0.9165 (tpp80) cc_final: 0.8338 (tpp80) REVERT: H 168 LYS cc_start: 0.7788 (pttt) cc_final: 0.6629 (pttt) REVERT: B 113 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: B 333 HIS cc_start: 0.8606 (t70) cc_final: 0.8089 (t70) REVERT: B 455 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7885 (tt0) outliers start: 35 outliers final: 30 residues processed: 144 average time/residue: 0.2734 time to fit residues: 59.0394 Evaluate side-chains 134 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 113 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.089837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058760 restraints weight = 49557.068| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.10 r_work: 0.3063 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15646 Z= 0.183 Angle : 0.591 8.188 21322 Z= 0.304 Chirality : 0.046 0.148 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.971 43.227 2124 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.43 % Allowed : 10.17 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1966 helix: 1.24 (0.35), residues: 222 sheet: -1.35 (0.18), residues: 756 loop : -1.03 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 119 HIS 0.003 0.001 HIS E 113 PHE 0.018 0.001 PHE H 115 TYR 0.018 0.002 TYR G 51 ARG 0.003 0.000 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 552) hydrogen bonds : angle 5.65747 ( 1686) SS BOND : bond 0.00257 ( 26) SS BOND : angle 0.87554 ( 52) covalent geometry : bond 0.00416 (15620) covalent geometry : angle 0.58994 (21270) *********************** 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 142 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9510 (m-30) cc_final: 0.9080 (p0) REVERT: F 18 ARG cc_start: 0.9151 (tpp80) cc_final: 0.8330 (tpp80) REVERT: F 168 LYS cc_start: 0.7848 (pttt) cc_final: 0.6663 (pttt) REVERT: A 333 HIS cc_start: 0.8571 (t70) cc_final: 0.8083 (t70) REVERT: A 399 MET cc_start: 0.9028 (mmt) cc_final: 0.8460 (mmt) REVERT: A 455 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: G 160 ASP cc_start: 0.9511 (m-30) cc_final: 0.9081 (p0) REVERT: H 18 ARG cc_start: 0.9150 (tpp80) cc_final: 0.8331 (tpp80) REVERT: H 168 LYS cc_start: 0.7849 (pttt) cc_final: 0.6667 (pttt) REVERT: B 113 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: B 333 HIS cc_start: 0.8556 (t70) cc_final: 0.8070 (t70) REVERT: B 399 MET cc_start: 0.9025 (mmt) cc_final: 0.8457 (mmt) REVERT: B 455 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7809 (tt0) outliers start: 25 outliers final: 22 residues processed: 136 average time/residue: 0.2811 time to fit residues: 57.2403 Evaluate side-chains 124 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 113 ASP 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 B residue 580 ILE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 150 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.090939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060175 restraints weight = 48754.437| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.21 r_work: 0.3105 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15646 Z= 0.122 Angle : 0.561 8.829 21322 Z= 0.288 Chirality : 0.045 0.148 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.763 39.099 2124 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 1966 helix: 1.44 (0.36), residues: 222 sheet: -1.13 (0.19), residues: 740 loop : -0.84 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 115 HIS 0.003 0.000 HIS G 113 PHE 0.018 0.001 PHE H 115 TYR 0.016 0.001 TYR E 51 ARG 0.002 0.000 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 552) hydrogen bonds : angle 5.46795 ( 1686) SS BOND : bond 0.00184 ( 26) SS BOND : angle 0.72403 ( 52) covalent geometry : bond 0.00275 (15620) covalent geometry : angle 0.56071 (21270) *********************** 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 144 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9532 (m-30) cc_final: 0.9128 (p0) REVERT: F 18 ARG cc_start: 0.9172 (tpp80) cc_final: 0.8346 (tpp80) REVERT: F 168 LYS cc_start: 0.7738 (pttt) cc_final: 0.6549 (pttt) REVERT: A 333 HIS cc_start: 0.8474 (t70) cc_final: 0.8126 (t70) REVERT: A 399 MET cc_start: 0.9007 (mmt) cc_final: 0.8602 (mmt) REVERT: A 455 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: G 160 ASP cc_start: 0.9532 (m-30) cc_final: 0.9126 (p0) REVERT: H 18 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8348 (tpp80) REVERT: H 168 LYS cc_start: 0.7737 (pttt) cc_final: 0.6551 (pttt) REVERT: B 113 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: B 333 HIS cc_start: 0.8476 (t70) cc_final: 0.8131 (t70) REVERT: B 399 MET cc_start: 0.8967 (mmt) cc_final: 0.8594 (mmt) REVERT: B 455 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7707 (tt0) outliers start: 25 outliers final: 18 residues processed: 138 average time/residue: 0.2780 time to fit residues: 57.3448 Evaluate side-chains 126 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.723 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 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 = 0.3932 r_free = 0.3932 target = 0.089961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059144 restraints weight = 48989.743| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 4.15 r_work: 0.3043 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15646 Z= 0.175 Angle : 0.583 8.068 21322 Z= 0.298 Chirality : 0.046 0.170 2418 Planarity : 0.004 0.050 2724 Dihedral : 4.789 37.982 2124 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.60 % Allowed : 10.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1966 helix: 1.48 (0.36), residues: 222 sheet: -1.11 (0.19), residues: 740 loop : -0.84 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.005 0.001 HIS E 113 PHE 0.017 0.001 PHE F 115 TYR 0.018 0.002 TYR A 291 ARG 0.002 0.000 ARG F 210 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 552) hydrogen bonds : angle 5.45833 ( 1686) SS BOND : bond 0.00276 ( 26) SS BOND : angle 1.60343 ( 52) covalent geometry : bond 0.00399 (15620) covalent geometry : angle 0.57853 (21270) *********************** 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 146 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9553 (m-30) cc_final: 0.9172 (p0) REVERT: F 168 LYS cc_start: 0.7822 (pttt) cc_final: 0.6679 (pttt) REVERT: A 318 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7760 (ptm160) REVERT: A 333 HIS cc_start: 0.8587 (t70) cc_final: 0.8022 (t70) REVERT: A 399 MET cc_start: 0.9030 (mmt) cc_final: 0.8647 (mmt) REVERT: A 455 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: G 160 ASP cc_start: 0.9552 (m-30) cc_final: 0.9171 (p0) REVERT: H 168 LYS cc_start: 0.7828 (pttt) cc_final: 0.6688 (pttt) REVERT: B 318 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7736 (ptm160) REVERT: B 333 HIS cc_start: 0.8576 (t70) cc_final: 0.8061 (t70) REVERT: B 399 MET cc_start: 0.9026 (mmt) cc_final: 0.8655 (mmt) REVERT: B 455 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7742 (tt0) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.3020 time to fit residues: 62.3914 Evaluate side-chains 135 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 318 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 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 B residue 580 ILE 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 91 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 160 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 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 = 0.3914 r_free = 0.3914 target = 0.089038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058253 restraints weight = 49608.603| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.97 r_work: 0.3013 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15646 Z= 0.224 Angle : 0.622 10.959 21322 Z= 0.317 Chirality : 0.046 0.256 2418 Planarity : 0.005 0.049 2724 Dihedral : 4.884 39.003 2124 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.77 % Allowed : 10.17 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1966 helix: 1.35 (0.35), residues: 224 sheet: -1.14 (0.19), residues: 758 loop : -0.77 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 35 HIS 0.006 0.001 HIS G 113 PHE 0.018 0.002 PHE F 115 TYR 0.025 0.002 TYR E 51 ARG 0.004 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 552) hydrogen bonds : angle 5.52882 ( 1686) SS BOND : bond 0.00290 ( 26) SS BOND : angle 1.49001 ( 52) covalent geometry : bond 0.00509 (15620) covalent geometry : angle 0.61799 (21270) ********************** 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 146 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 160 ASP cc_start: 0.9543 (m-30) cc_final: 0.9142 (p0) REVERT: F 168 LYS cc_start: 0.7824 (pttt) cc_final: 0.6658 (pttt) REVERT: A 290 PHE cc_start: 0.8253 (m-80) cc_final: 0.7731 (m-80) REVERT: A 318 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6268 (ptp90) REVERT: A 333 HIS cc_start: 0.8632 (t70) cc_final: 0.7964 (t70) REVERT: A 399 MET cc_start: 0.9054 (mmt) cc_final: 0.8702 (mmt) REVERT: A 455 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: G 160 ASP cc_start: 0.9543 (m-30) cc_final: 0.9141 (p0) REVERT: H 168 LYS cc_start: 0.7829 (pttt) cc_final: 0.6662 (pttt) REVERT: B 318 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6252 (ptp90) REVERT: B 333 HIS cc_start: 0.8633 (t70) cc_final: 0.7988 (t70) REVERT: B 399 MET cc_start: 0.9042 (mmt) cc_final: 0.8697 (mmt) REVERT: B 455 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7837 (tt0) outliers start: 31 outliers final: 27 residues processed: 139 average time/residue: 0.2812 time to fit residues: 59.2541 Evaluate side-chains 134 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 110 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 455 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain D residue 101 ILE 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 75 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.089711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.058801 restraints weight = 49341.683| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.22 r_work: 0.3066 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15646 Z= 0.173 Angle : 0.593 8.509 21322 Z= 0.303 Chirality : 0.046 0.181 2418 Planarity : 0.004 0.048 2724 Dihedral : 4.823 38.068 2124 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.71 % Allowed : 10.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1966 helix: 1.43 (0.36), residues: 222 sheet: -1.14 (0.19), residues: 752 loop : -0.73 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 119 HIS 0.005 0.001 HIS E 113 PHE 0.019 0.001 PHE F 115 TYR 0.021 0.002 TYR E 51 ARG 0.004 0.000 ARG B 338 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 552) hydrogen bonds : angle 5.44443 ( 1686) SS BOND : bond 0.00231 ( 26) SS BOND : angle 1.36691 ( 52) covalent geometry : bond 0.00395 (15620) covalent geometry : angle 0.59034 (21270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9346.84 seconds wall clock time: 164 minutes 21.12 seconds (9861.12 seconds total)