Starting phenix.real_space_refine on Thu Sep 18 00:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rex_19111/09_2025/8rex_19111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rex_19111/09_2025/8rex_19111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rex_19111/09_2025/8rex_19111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rex_19111/09_2025/8rex_19111.map" model { file = "/net/cci-nas-00/data/ceres_data/8rex_19111/09_2025/8rex_19111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rex_19111/09_2025/8rex_19111.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 66 5.16 5 C 7809 2.51 5 N 2122 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12357 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1672 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 834 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 94} Chain breaks: 1 Chain: "C" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1662 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 91} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3908 Classifications: {'peptide': 509} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 776 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 911 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 780 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.54, per 1000 atoms: 0.29 Number of scatterers: 12357 At special positions: 0 Unit cell: (100.8, 154.08, 156.96, 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 66 16.00 O 2360 8.00 N 2122 7.00 C 7809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 285 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS E 351 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 356 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 387 " distance=2.03 Simple disulfide: pdb=" SG CYS D 326 " - pdb=" SG CYS D 389 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 437 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 401 " - " ASN A 176 " " NAG E1000 " - " ASN E 272 " " NAG J 1 " - " ASN A 136 " " NAG K 1 " - " ASN C 136 " " NAG L 1 " - " ASN E 204 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 689.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 28 sheets defined 13.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 removed outlier: 3.597A pdb=" N LEU A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.862A pdb=" N LEU A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.731A pdb=" N LYS A 125 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'B' and resid 281 through 287 removed outlier: 4.258A pdb=" N CYS B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 346 removed outlier: 3.510A pdb=" N TYR B 343 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 344 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN B 345 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 346 " --> pdb=" O TYR B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 346' Processing helix chain 'C' and resid 37 through 57 removed outlier: 3.947A pdb=" N VAL C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.993A pdb=" N ALA C 268 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 342 through 347 Processing helix chain 'E' and resid 93 through 97 Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 138 through 147 removed outlier: 3.682A pdb=" N LEU E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.368A pdb=" N PHE E 170 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP E 171 " --> pdb=" O HIS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 removed outlier: 3.711A pdb=" N LEU E 336 " --> pdb=" O PRO E 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.742A pdb=" N TYR G 51 " --> pdb=" O PHE G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 75 removed outlier: 4.210A pdb=" N GLY G 75 " --> pdb=" O ILE G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 75' Processing helix chain 'G' and resid 81 through 84 removed outlier: 3.506A pdb=" N LYS G 84 " --> pdb=" O ASP G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 84' Processing helix chain 'G' and resid 106 through 110 removed outlier: 3.877A pdb=" N THR G 110 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 3.549A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.541A pdb=" N LYS H 84 " --> pdb=" O ASP H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.126A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.569A pdb=" N PHE A 257 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 106 " --> pdb=" O GLN D 378 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 378 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 108 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL D 376 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 10.606A pdb=" N ARG A 110 " --> pdb=" O PRO D 374 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL D 370 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN D 381 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU D 362 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 313 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR D 369 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE D 311 " --> pdb=" O TYR D 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 136 removed outlier: 3.659A pdb=" N GLN A 172 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 180 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'B' and resid 294 through 295 removed outlier: 3.939A pdb=" N CYS B 294 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 299 through 301 Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 313 removed outlier: 7.298A pdb=" N ILE B 311 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR B 369 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS B 356 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N CYS B 387 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ARG B 385 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 360 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 383 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 362 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN B 381 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 370 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.829A pdb=" N PHE C 257 " --> pdb=" O ARG C 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 130 through 136 removed outlier: 5.391A pdb=" N GLY C 216 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 168 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 185 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY C 183 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN C 172 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR C 181 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 294 through 296 removed outlier: 3.834A pdb=" N CYS D 294 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 323 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 321 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AB2, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AB3, first strand: chain 'E' and resid 34 through 35 removed outlier: 6.910A pdb=" N ALA E 34 " --> pdb=" O TYR E 56 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU E 79 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA E 106 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 133 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU E 179 " --> pdb=" O ASN E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 164 through 165 Processing sheet with id=AB5, first strand: chain 'E' and resid 213 through 214 removed outlier: 6.454A pdb=" N ILE E 213 " --> pdb=" O GLN E 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 344 through 348 removed outlier: 6.978A pdb=" N LEU E 345 " --> pdb=" O ASP E 370 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER E 372 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU E 347 " --> pdb=" O SER E 372 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 395 " --> pdb=" O LEU E 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 355 through 357 removed outlier: 3.676A pdb=" N GLU E 380 " --> pdb=" O PHE E 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 415 through 418 removed outlier: 6.710A pdb=" N LEU E 416 " --> pdb=" O ASN E 450 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ALA E 452 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU E 418 " --> pdb=" O ALA E 452 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 475 " --> pdb=" O MET E 451 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 498 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 474 " --> pdb=" O GLU E 498 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN E 500 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU E 497 " --> pdb=" O ARG E 519 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN E 521 " --> pdb=" O LEU E 497 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 520 " --> pdb=" O VAL E 541 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP E 543 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.571A pdb=" N MET F 29 " --> pdb=" O HIS F 126 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU F 67 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.571A pdb=" N MET F 29 " --> pdb=" O HIS F 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 37 through 42 Processing sheet with id=AC3, first strand: chain 'G' and resid 22 through 26 removed outlier: 4.010A pdb=" N SER G 40 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU G 37 " --> pdb=" O MET G 102 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU G 100 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 98 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP G 92 " --> pdb=" O THR G 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 77 through 79 removed outlier: 6.521A pdb=" N TRP G 55 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY G 69 " --> pdb=" O MET G 53 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET G 53 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP G 129 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 77 through 79 removed outlier: 6.521A pdb=" N TRP G 55 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY G 69 " --> pdb=" O MET G 53 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET G 53 " --> pdb=" O GLY G 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.504A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.632A pdb=" N GLY H 29 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR H 137 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR H 134 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 28 through 29 removed outlier: 3.786A pdb=" N MET I 29 " --> pdb=" O HIS I 126 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU I 54 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR I 70 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP I 56 " --> pdb=" O VAL I 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 28 through 29 removed outlier: 3.786A pdb=" N MET I 29 " --> pdb=" O HIS I 126 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS I 111 " --> pdb=" O VAL I 120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 36 through 42 removed outlier: 3.686A pdb=" N VAL I 37 " --> pdb=" O ILE I 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 96 " --> pdb=" O VAL I 37 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 840 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: 2.42 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3559 1.33 - 1.45: 2134 1.45 - 1.57: 6833 1.57 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 12617 Sorted by residual: bond pdb=" N TYR F 53 " pdb=" CA TYR F 53 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.27e-02 6.20e+03 8.72e+00 bond pdb=" CA ALA D 352 " pdb=" CB ALA D 352 " ideal model delta sigma weight residual 1.532 1.494 0.038 1.33e-02 5.65e+03 8.28e+00 bond pdb=" C VAL C 41 " pdb=" N LYS C 42 " ideal model delta sigma weight residual 1.334 1.298 0.036 1.27e-02 6.20e+03 8.08e+00 bond pdb=" N VAL C 41 " pdb=" CA VAL C 41 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.01e+00 bond pdb=" N TRP E 248 " pdb=" CA TRP E 248 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.83e+00 ... (remaining 12612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 16354 1.77 - 3.54: 633 3.54 - 5.31: 125 5.31 - 7.08: 29 7.08 - 8.85: 7 Bond angle restraints: 17148 Sorted by residual: angle pdb=" N ALA C 48 " pdb=" CA ALA C 48 " pdb=" C ALA C 48 " ideal model delta sigma weight residual 112.54 106.78 5.76 1.22e+00 6.72e-01 2.23e+01 angle pdb=" CA TYR F 53 " pdb=" C TYR F 53 " pdb=" O TYR F 53 " ideal model delta sigma weight residual 120.54 115.97 4.57 1.04e+00 9.25e-01 1.93e+01 angle pdb=" C THR G 137 " pdb=" N VAL G 138 " pdb=" CA VAL G 138 " ideal model delta sigma weight residual 122.63 117.53 5.10 1.19e+00 7.06e-01 1.84e+01 angle pdb=" C ASP E 396 " pdb=" N ASN E 397 " pdb=" CA ASN E 397 " ideal model delta sigma weight residual 121.71 115.89 5.82 1.39e+00 5.18e-01 1.76e+01 angle pdb=" CA ARG C 45 " pdb=" C ARG C 45 " pdb=" O ARG C 45 " ideal model delta sigma weight residual 120.42 116.04 4.38 1.06e+00 8.90e-01 1.71e+01 ... (remaining 17143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6923 17.76 - 35.52: 621 35.52 - 53.29: 99 53.29 - 71.05: 20 71.05 - 88.81: 15 Dihedral angle restraints: 7678 sinusoidal: 3113 harmonic: 4565 Sorted by residual: dihedral pdb=" CB CYS D 293 " pdb=" SG CYS D 293 " pdb=" SG CYS D 356 " pdb=" CB CYS D 356 " ideal model delta sinusoidal sigma weight residual -86.00 -157.19 71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS F 41 " pdb=" SG CYS F 41 " pdb=" SG CYS F 109 " pdb=" CB CYS F 109 " ideal model delta sinusoidal sigma weight residual 93.00 155.98 -62.98 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CA LYS G 106 " pdb=" C LYS G 106 " pdb=" N SER G 107 " pdb=" CA SER G 107 " ideal model delta harmonic sigma weight residual 180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 7675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1468 0.050 - 0.100: 380 0.100 - 0.150: 98 0.150 - 0.199: 9 0.199 - 0.249: 6 Chirality restraints: 1961 Sorted by residual: chirality pdb=" CA ARG C 43 " pdb=" N ARG C 43 " pdb=" C ARG C 43 " pdb=" CB ARG C 43 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE E 443 " pdb=" CA ILE E 443 " pdb=" CG1 ILE E 443 " pdb=" CG2 ILE E 443 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA LEU H 39 " pdb=" N LEU H 39 " pdb=" C LEU H 39 " pdb=" CB LEU H 39 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1958 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG H 38 " -0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ARG H 38 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG H 38 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU H 39 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 330 " 0.030 2.00e-02 2.50e+03 1.59e-02 6.30e+00 pdb=" CG TRP D 330 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 330 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 330 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 330 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP D 330 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 330 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 330 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 330 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 330 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 61 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO C 62 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.033 5.00e-02 4.00e+02 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2595 2.78 - 3.31: 11170 3.31 - 3.84: 20858 3.84 - 4.37: 24424 4.37 - 4.90: 42273 Nonbonded interactions: 101320 Sorted by model distance: nonbonded pdb=" O MET C 113 " pdb=" NH1 ARG C 255 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR H 54 " pdb=" OD1 ASP H 118 " model vdw 2.268 3.040 nonbonded pdb=" OE1 GLN E 85 " pdb=" NH2 ARG E 109 " model vdw 2.271 3.120 nonbonded pdb=" O PRO A 145 " pdb=" OH TYR H 52 " model vdw 2.273 3.040 nonbonded pdb=" O SER C 83 " pdb=" NH1 ARG C 156 " model vdw 2.289 3.120 ... (remaining 101315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 86 or resid 102 through 115 or (resid 116 and ( \ name N or name CA or name C or name O or name CB )) or resid 117 through 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 124 \ or (resid 125 and (name N or name CA or name C or name O or name CB )) or resid \ 126 through 227 or (resid 228 and (name N or name CA or name C or name O or nam \ e CB )) or resid 229 through 240 or resid 254 through 268)) selection = (chain 'C' and (resid 33 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 65 or resid 72 through 86 or resid \ 102 through 268)) } ncs_group { reference = (chain 'B' and (resid 290 through 303 or (resid 304 and (name N or name CA or na \ me C or name O or name CB )) or resid 305 through 371 or (resid 372 through 373 \ and (name N or name CA or name C or name O or name CB )) or resid 374 through 39 \ 0)) selection = (chain 'D' and (resid 290 through 332 or resid 340 through 390)) } ncs_group { reference = chain 'F' selection = (chain 'I' and (resid 22 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 130)) } ncs_group { reference = (chain 'G' and (resid 21 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 140)) selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 8.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.004 0.051 12640 Z= 0.223 Angle : 0.838 11.243 17202 Z= 0.451 Chirality : 0.049 0.249 1961 Planarity : 0.006 0.059 2203 Dihedral : 13.846 88.811 4705 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.21), residues: 1556 helix: -1.54 (0.39), residues: 141 sheet: -0.59 (0.26), residues: 411 loop : -1.34 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 43 TYR 0.030 0.002 TYR G 79 PHE 0.012 0.001 PHE H 87 TRP 0.037 0.002 TRP D 330 HIS 0.008 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00435 (12617) covalent geometry : angle 0.83013 (17148) SS BOND : bond 0.00246 ( 15) SS BOND : angle 1.25459 ( 30) hydrogen bonds : bond 0.25792 ( 306) hydrogen bonds : angle 10.06101 ( 840) link_BETA1-4 : bond 0.00431 ( 3) link_BETA1-4 : angle 1.45175 ( 9) link_NAG-ASN : bond 0.00396 ( 5) link_NAG-ASN : angle 3.59079 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 0.526 Fit side-chains REVERT: A 180 ARG cc_start: 0.7858 (ptm-80) cc_final: 0.7627 (ptm-80) REVERT: A 230 ASN cc_start: 0.7394 (m110) cc_final: 0.6979 (m-40) REVERT: C 83 SER cc_start: 0.8127 (m) cc_final: 0.7904 (m) REVERT: E 235 GLN cc_start: 0.6103 (pt0) cc_final: 0.5862 (tm-30) REVERT: E 244 PHE cc_start: 0.8304 (m-80) cc_final: 0.8058 (m-80) REVERT: E 250 ASP cc_start: 0.7735 (m-30) cc_final: 0.7348 (m-30) REVERT: H 22 GLN cc_start: 0.7861 (pm20) cc_final: 0.7456 (pp30) outliers start: 1 outliers final: 2 residues processed: 272 average time/residue: 0.5125 time to fit residues: 153.9699 Evaluate side-chains 211 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain E residue 62 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 230 ASN A 233 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN D 292 ASN D 346 HIS E 178 GLN E 199 HIS F 47 ASN F 71 ASN G 104 ASN H 104 ASN ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.174191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122837 restraints weight = 17487.383| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.54 r_work: 0.3631 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12640 Z= 0.190 Angle : 0.699 11.770 17202 Z= 0.347 Chirality : 0.044 0.159 1961 Planarity : 0.005 0.049 2203 Dihedral : 6.484 55.469 1886 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.96 % Allowed : 12.15 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.21), residues: 1556 helix: -1.23 (0.40), residues: 148 sheet: -0.60 (0.25), residues: 445 loop : -1.22 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 303 TYR 0.024 0.002 TYR F 112 PHE 0.018 0.002 PHE H 87 TRP 0.018 0.002 TRP H 55 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00457 (12617) covalent geometry : angle 0.68809 (17148) SS BOND : bond 0.00329 ( 15) SS BOND : angle 1.39918 ( 30) hydrogen bonds : bond 0.04320 ( 306) hydrogen bonds : angle 7.20940 ( 840) link_BETA1-4 : bond 0.00166 ( 3) link_BETA1-4 : angle 1.45328 ( 9) link_NAG-ASN : bond 0.00463 ( 5) link_NAG-ASN : angle 3.76959 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.498 Fit side-chains REVERT: A 154 GLU cc_start: 0.7685 (tt0) cc_final: 0.7483 (tt0) REVERT: A 180 ARG cc_start: 0.8116 (ptm-80) cc_final: 0.7832 (ptm-80) REVERT: A 230 ASN cc_start: 0.7429 (m-40) cc_final: 0.6864 (m-40) REVERT: B 303 ARG cc_start: 0.8581 (mmm160) cc_final: 0.8256 (tpp-160) REVERT: B 313 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: C 39 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6977 (tm-30) REVERT: C 173 LYS cc_start: 0.7454 (tmtt) cc_final: 0.7188 (tmtt) REVERT: C 254 ASN cc_start: 0.5348 (t0) cc_final: 0.5116 (t0) REVERT: E 80 ASP cc_start: 0.6523 (m-30) cc_final: 0.5946 (m-30) REVERT: E 83 ASP cc_start: 0.8854 (t70) cc_final: 0.8539 (t70) REVERT: E 187 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: E 235 GLN cc_start: 0.6218 (pt0) cc_final: 0.5668 (tm-30) REVERT: E 349 ARG cc_start: 0.5569 (tmm160) cc_final: 0.5193 (tmt170) REVERT: F 90 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8134 (t0) REVERT: G 54 TYR cc_start: 0.7898 (m-80) cc_final: 0.7690 (m-80) REVERT: G 103 ASN cc_start: 0.8266 (t0) cc_final: 0.8062 (t0) REVERT: G 109 ASP cc_start: 0.8297 (m-30) cc_final: 0.8016 (m-30) REVERT: G 135 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7833 (tm-30) REVERT: H 22 GLN cc_start: 0.7873 (pm20) cc_final: 0.7231 (pp30) REVERT: H 55 TRP cc_start: 0.8791 (m100) cc_final: 0.8543 (m100) REVERT: H 99 TYR cc_start: 0.7620 (m-80) cc_final: 0.7033 (m-80) outliers start: 40 outliers final: 18 residues processed: 242 average time/residue: 0.5549 time to fit residues: 146.8787 Evaluate side-chains 227 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 0.0030 chunk 19 optimal weight: 1.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS D 345 GLN D 346 HIS E 78 HIS E 199 HIS H 101 GLN H 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.176407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125351 restraints weight = 17550.723| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.66 r_work: 0.3679 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12640 Z= 0.119 Angle : 0.634 11.111 17202 Z= 0.309 Chirality : 0.042 0.152 1961 Planarity : 0.004 0.048 2203 Dihedral : 5.906 54.816 1882 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.74 % Allowed : 16.30 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.21), residues: 1556 helix: -0.60 (0.43), residues: 142 sheet: -0.56 (0.25), residues: 445 loop : -1.19 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 82 TYR 0.017 0.001 TYR F 112 PHE 0.010 0.001 PHE D 321 TRP 0.011 0.001 TRP G 66 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00279 (12617) covalent geometry : angle 0.62368 (17148) SS BOND : bond 0.00216 ( 15) SS BOND : angle 0.96852 ( 30) hydrogen bonds : bond 0.03703 ( 306) hydrogen bonds : angle 6.55648 ( 840) link_BETA1-4 : bond 0.00202 ( 3) link_BETA1-4 : angle 1.31015 ( 9) link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 3.69245 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7689 (tt0) cc_final: 0.7457 (tt0) REVERT: A 165 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7527 (tp30) REVERT: A 174 TYR cc_start: 0.7751 (m-10) cc_final: 0.7501 (m-10) REVERT: A 180 ARG cc_start: 0.8047 (ptm-80) cc_final: 0.7823 (ptm-80) REVERT: A 230 ASN cc_start: 0.7355 (m-40) cc_final: 0.6913 (m110) REVERT: A 231 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7959 (tptm) REVERT: B 290 GLU cc_start: 0.5992 (tm-30) cc_final: 0.5509 (tm-30) REVERT: B 303 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8211 (tpp-160) REVERT: B 343 TYR cc_start: 0.8172 (m-80) cc_final: 0.7965 (m-80) REVERT: C 38 MET cc_start: 0.6466 (tpp) cc_final: 0.6234 (tpp) REVERT: C 39 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7088 (tm-30) REVERT: C 173 LYS cc_start: 0.7485 (tmtt) cc_final: 0.7258 (tmtt) REVERT: E 78 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7068 (t70) REVERT: E 80 ASP cc_start: 0.6502 (m-30) cc_final: 0.5547 (m-30) REVERT: E 83 ASP cc_start: 0.8861 (t70) cc_final: 0.8466 (t70) REVERT: E 114 MET cc_start: 0.5435 (tmt) cc_final: 0.5182 (tmt) REVERT: E 187 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7366 (mtm) REVERT: E 235 GLN cc_start: 0.6188 (pt0) cc_final: 0.5592 (tm-30) REVERT: E 349 ARG cc_start: 0.5663 (tmm160) cc_final: 0.5128 (tmt170) REVERT: F 90 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8120 (t0) REVERT: G 54 TYR cc_start: 0.7820 (m-80) cc_final: 0.7618 (m-80) REVERT: G 102 MET cc_start: 0.7974 (mpp) cc_final: 0.7489 (mtt) REVERT: G 109 ASP cc_start: 0.8146 (m-30) cc_final: 0.7818 (m-30) REVERT: G 135 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7799 (tm-30) REVERT: H 22 GLN cc_start: 0.7880 (pm20) cc_final: 0.7312 (pp30) REVERT: H 55 TRP cc_start: 0.8819 (m100) cc_final: 0.8594 (m100) REVERT: H 99 TYR cc_start: 0.7587 (m-80) cc_final: 0.7029 (m-80) REVERT: I 91 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7264 (tm) outliers start: 37 outliers final: 17 residues processed: 233 average time/residue: 0.5006 time to fit residues: 129.1716 Evaluate side-chains 226 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 0.0030 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN E 199 HIS H 101 GLN H 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.174770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123940 restraints weight = 17411.732| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.54 r_work: 0.3658 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12640 Z= 0.140 Angle : 0.619 10.997 17202 Z= 0.304 Chirality : 0.042 0.147 1961 Planarity : 0.004 0.048 2203 Dihedral : 5.750 55.246 1882 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.19 % Allowed : 17.26 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.21), residues: 1556 helix: -0.39 (0.43), residues: 142 sheet: -0.55 (0.25), residues: 447 loop : -1.13 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 180 TYR 0.017 0.002 TYR F 70 PHE 0.014 0.001 PHE H 87 TRP 0.010 0.001 TRP D 330 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00335 (12617) covalent geometry : angle 0.60759 (17148) SS BOND : bond 0.00294 ( 15) SS BOND : angle 1.11329 ( 30) hydrogen bonds : bond 0.03509 ( 306) hydrogen bonds : angle 6.28190 ( 840) link_BETA1-4 : bond 0.00217 ( 3) link_BETA1-4 : angle 1.30804 ( 9) link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 3.68270 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.507 Fit side-chains REVERT: A 154 GLU cc_start: 0.7662 (tt0) cc_final: 0.7435 (tt0) REVERT: A 165 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7550 (tp30) REVERT: A 230 ASN cc_start: 0.7388 (m-40) cc_final: 0.6938 (m110) REVERT: B 290 GLU cc_start: 0.5997 (tm-30) cc_final: 0.5518 (tm-30) REVERT: C 39 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 83 SER cc_start: 0.8665 (OUTLIER) cc_final: 0.8411 (m) REVERT: C 173 LYS cc_start: 0.7491 (tmtt) cc_final: 0.7215 (tmtt) REVERT: E 78 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: E 80 ASP cc_start: 0.6651 (m-30) cc_final: 0.5231 (m-30) REVERT: E 83 ASP cc_start: 0.8875 (t70) cc_final: 0.8424 (t70) REVERT: E 85 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7912 (mp10) REVERT: E 114 MET cc_start: 0.5387 (tmt) cc_final: 0.5090 (tmt) REVERT: E 187 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7408 (mtm) REVERT: E 235 GLN cc_start: 0.6222 (pt0) cc_final: 0.5553 (tm-30) REVERT: F 90 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8113 (t0) REVERT: G 32 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8622 (pp30) REVERT: G 53 MET cc_start: 0.7026 (mmp) cc_final: 0.6695 (mmp) REVERT: G 68 SER cc_start: 0.8608 (t) cc_final: 0.8396 (m) REVERT: G 109 ASP cc_start: 0.8179 (m-30) cc_final: 0.7822 (m-30) REVERT: G 135 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7788 (tm-30) REVERT: H 22 GLN cc_start: 0.7861 (pm20) cc_final: 0.7317 (pp30) REVERT: H 99 TYR cc_start: 0.7686 (m-80) cc_final: 0.7139 (m-80) REVERT: I 37 VAL cc_start: 0.6433 (p) cc_final: 0.6188 (t) REVERT: I 91 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7174 (tm) outliers start: 43 outliers final: 24 residues processed: 235 average time/residue: 0.4764 time to fit residues: 124.2953 Evaluate side-chains 230 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LYS Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 5.9990 chunk 13 optimal weight: 0.0270 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 101 optimal weight: 30.0000 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 199 HIS E 279 GLN G 103 ASN H 101 GLN H 104 ASN I 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.174448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122774 restraints weight = 17631.898| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.77 r_work: 0.3628 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12640 Z= 0.137 Angle : 0.624 10.922 17202 Z= 0.303 Chirality : 0.042 0.145 1961 Planarity : 0.004 0.048 2203 Dihedral : 5.611 54.912 1882 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.93 % Allowed : 18.07 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.21), residues: 1556 helix: -0.29 (0.44), residues: 142 sheet: -0.61 (0.24), residues: 448 loop : -1.07 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 303 TYR 0.022 0.002 TYR F 70 PHE 0.011 0.001 PHE H 87 TRP 0.028 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00327 (12617) covalent geometry : angle 0.61347 (17148) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.04194 ( 30) hydrogen bonds : bond 0.03386 ( 306) hydrogen bonds : angle 6.03113 ( 840) link_BETA1-4 : bond 0.00221 ( 3) link_BETA1-4 : angle 1.29776 ( 9) link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 3.67610 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7689 (tt0) cc_final: 0.7430 (tt0) REVERT: A 165 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: A 230 ASN cc_start: 0.7236 (m-40) cc_final: 0.6778 (m110) REVERT: A 231 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7955 (tptm) REVERT: B 290 GLU cc_start: 0.5980 (tm-30) cc_final: 0.5463 (tm-30) REVERT: B 303 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8113 (tpp-160) REVERT: C 83 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8536 (m) REVERT: C 173 LYS cc_start: 0.7462 (tmtt) cc_final: 0.7154 (tmtt) REVERT: E 78 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7214 (t70) REVERT: E 80 ASP cc_start: 0.6789 (m-30) cc_final: 0.5673 (m-30) REVERT: E 83 ASP cc_start: 0.8900 (t70) cc_final: 0.8425 (t70) REVERT: E 85 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7924 (mp10) REVERT: E 114 MET cc_start: 0.5366 (tmt) cc_final: 0.5115 (tmt) REVERT: E 187 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: E 235 GLN cc_start: 0.6130 (pt0) cc_final: 0.5426 (tm-30) REVERT: E 451 MET cc_start: 0.4421 (ppp) cc_final: 0.3170 (tpt) REVERT: F 90 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7965 (t0) REVERT: G 53 MET cc_start: 0.7179 (mmp) cc_final: 0.6729 (mmp) REVERT: G 102 MET cc_start: 0.8480 (mpp) cc_final: 0.7910 (mtp) REVERT: G 109 ASP cc_start: 0.8155 (m-30) cc_final: 0.7784 (m-30) REVERT: G 135 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7872 (tm-30) REVERT: H 22 GLN cc_start: 0.7808 (pm20) cc_final: 0.7217 (pp30) REVERT: H 99 TYR cc_start: 0.7694 (m-80) cc_final: 0.7166 (m-80) REVERT: I 91 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7089 (tm) outliers start: 53 outliers final: 24 residues processed: 238 average time/residue: 0.4694 time to fit residues: 124.1635 Evaluate side-chains 239 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LYS Chi-restraints excluded: chain I residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 139 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 94 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 199 HIS E 279 GLN H 101 GLN H 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.174520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123505 restraints weight = 17543.348| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.60 r_work: 0.3641 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12640 Z= 0.131 Angle : 0.624 10.879 17202 Z= 0.303 Chirality : 0.041 0.143 1961 Planarity : 0.004 0.049 2203 Dihedral : 5.512 54.668 1882 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.85 % Allowed : 18.96 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.21), residues: 1556 helix: -0.23 (0.44), residues: 142 sheet: -0.47 (0.25), residues: 445 loop : -1.03 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 180 TYR 0.019 0.001 TYR A 181 PHE 0.008 0.001 PHE D 321 TRP 0.016 0.001 TRP H 55 HIS 0.011 0.001 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00314 (12617) covalent geometry : angle 0.61291 (17148) SS BOND : bond 0.00286 ( 15) SS BOND : angle 1.08327 ( 30) hydrogen bonds : bond 0.03298 ( 306) hydrogen bonds : angle 5.92733 ( 840) link_BETA1-4 : bond 0.00275 ( 3) link_BETA1-4 : angle 1.29385 ( 9) link_NAG-ASN : bond 0.00357 ( 5) link_NAG-ASN : angle 3.65162 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.7596 (tpt) cc_final: 0.7278 (tpt) REVERT: A 154 GLU cc_start: 0.7662 (tt0) cc_final: 0.7407 (tt0) REVERT: A 165 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: A 187 LEU cc_start: 0.8564 (mm) cc_final: 0.8105 (mt) REVERT: A 230 ASN cc_start: 0.7279 (m-40) cc_final: 0.6814 (m110) REVERT: A 231 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7962 (tptm) REVERT: B 290 GLU cc_start: 0.6044 (tm-30) cc_final: 0.5690 (tm-30) REVERT: B 303 ARG cc_start: 0.8400 (mmm160) cc_final: 0.8116 (tpp-160) REVERT: C 39 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7049 (tm-30) REVERT: C 78 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8159 (mt) REVERT: C 173 LYS cc_start: 0.7480 (tmtt) cc_final: 0.7162 (tmtt) REVERT: D 301 ASP cc_start: 0.7711 (t0) cc_final: 0.7460 (t0) REVERT: E 60 ASN cc_start: 0.8995 (t0) cc_final: 0.8700 (t0) REVERT: E 78 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7171 (t70) REVERT: E 80 ASP cc_start: 0.6688 (m-30) cc_final: 0.5706 (m-30) REVERT: E 83 ASP cc_start: 0.8863 (t70) cc_final: 0.8252 (t70) REVERT: E 85 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7917 (mp10) REVERT: E 114 MET cc_start: 0.5417 (tmt) cc_final: 0.5136 (tmt) REVERT: E 187 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7902 (mpp) REVERT: E 235 GLN cc_start: 0.6139 (pt0) cc_final: 0.5439 (tm-30) REVERT: E 451 MET cc_start: 0.4753 (ppp) cc_final: 0.3252 (tpt) REVERT: F 90 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7946 (t0) REVERT: G 32 GLN cc_start: 0.9061 (tp40) cc_final: 0.8350 (pp30) REVERT: G 53 MET cc_start: 0.7266 (mmp) cc_final: 0.6850 (mmp) REVERT: G 79 TYR cc_start: 0.8339 (m-80) cc_final: 0.8020 (m-80) REVERT: G 102 MET cc_start: 0.8465 (mpp) cc_final: 0.7913 (mtp) REVERT: G 109 ASP cc_start: 0.8136 (m-30) cc_final: 0.7774 (m-30) REVERT: G 135 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7871 (tm-30) REVERT: H 22 GLN cc_start: 0.7781 (pm20) cc_final: 0.7221 (pp30) REVERT: H 92 ASP cc_start: 0.6754 (t0) cc_final: 0.6490 (t0) REVERT: H 99 TYR cc_start: 0.7674 (m-80) cc_final: 0.7125 (m-80) REVERT: I 91 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7142 (tm) outliers start: 52 outliers final: 22 residues processed: 242 average time/residue: 0.4764 time to fit residues: 127.8929 Evaluate side-chains 238 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 78 HIS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 47 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS E 279 GLN H 101 GLN H 104 ASN I 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.174302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123576 restraints weight = 17450.964| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.50 r_work: 0.3643 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12640 Z= 0.136 Angle : 0.643 10.895 17202 Z= 0.309 Chirality : 0.041 0.146 1961 Planarity : 0.004 0.051 2203 Dihedral : 5.447 54.489 1882 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.41 % Allowed : 19.70 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1556 helix: -0.18 (0.44), residues: 142 sheet: -0.44 (0.24), residues: 452 loop : -1.02 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 180 TYR 0.034 0.002 TYR F 70 PHE 0.009 0.001 PHE H 87 TRP 0.014 0.001 TRP H 55 HIS 0.007 0.001 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00327 (12617) covalent geometry : angle 0.63248 (17148) SS BOND : bond 0.00281 ( 15) SS BOND : angle 1.17867 ( 30) hydrogen bonds : bond 0.03275 ( 306) hydrogen bonds : angle 5.85275 ( 840) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 1.29334 ( 9) link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 3.64350 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7193 (tpt) REVERT: A 154 GLU cc_start: 0.7664 (tt0) cc_final: 0.7406 (tt0) REVERT: A 165 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 187 LEU cc_start: 0.8567 (mm) cc_final: 0.8119 (mt) REVERT: A 230 ASN cc_start: 0.7318 (m-40) cc_final: 0.6839 (m110) REVERT: A 231 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7966 (tptm) REVERT: B 290 GLU cc_start: 0.6000 (tm-30) cc_final: 0.5622 (tm-30) REVERT: B 292 ASN cc_start: 0.7749 (t0) cc_final: 0.7470 (OUTLIER) REVERT: B 303 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8105 (tpp-160) REVERT: C 113 MET cc_start: 0.8864 (ptm) cc_final: 0.8619 (ttm) REVERT: E 60 ASN cc_start: 0.8983 (t0) cc_final: 0.8689 (t0) REVERT: E 78 HIS cc_start: 0.7689 (t-90) cc_final: 0.7070 (t-90) REVERT: E 83 ASP cc_start: 0.8846 (t70) cc_final: 0.8253 (t70) REVERT: E 85 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7907 (mp10) REVERT: E 114 MET cc_start: 0.5410 (tmt) cc_final: 0.5190 (tmt) REVERT: E 187 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7912 (mpp) REVERT: E 235 GLN cc_start: 0.6164 (pt0) cc_final: 0.5443 (tm-30) REVERT: E 451 MET cc_start: 0.4820 (ppp) cc_final: 0.3264 (tpt) REVERT: F 90 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7938 (t0) REVERT: G 53 MET cc_start: 0.7285 (mmp) cc_final: 0.6811 (mmp) REVERT: G 102 MET cc_start: 0.8508 (mpp) cc_final: 0.8123 (mtp) REVERT: G 109 ASP cc_start: 0.8117 (m-30) cc_final: 0.7738 (m-30) REVERT: G 135 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7838 (tm-30) REVERT: H 22 GLN cc_start: 0.7804 (pm20) cc_final: 0.7130 (pp30) REVERT: H 92 ASP cc_start: 0.6744 (t0) cc_final: 0.6521 (t0) REVERT: H 99 TYR cc_start: 0.7701 (m-80) cc_final: 0.7164 (m-80) REVERT: I 91 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7133 (tm) outliers start: 46 outliers final: 26 residues processed: 237 average time/residue: 0.4735 time to fit residues: 124.0548 Evaluate side-chains 234 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LYS Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.0870 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 92 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS E 279 GLN H 101 GLN H 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.175088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124534 restraints weight = 17351.379| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 3.58 r_work: 0.3671 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12640 Z= 0.116 Angle : 0.643 10.919 17202 Z= 0.309 Chirality : 0.041 0.148 1961 Planarity : 0.004 0.053 2203 Dihedral : 5.323 54.137 1882 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.59 % Allowed : 21.56 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.21), residues: 1556 helix: -0.13 (0.44), residues: 142 sheet: -0.48 (0.24), residues: 445 loop : -0.97 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 180 TYR 0.022 0.001 TYR F 70 PHE 0.010 0.001 PHE D 321 TRP 0.013 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00279 (12617) covalent geometry : angle 0.63359 (17148) SS BOND : bond 0.00235 ( 15) SS BOND : angle 0.96379 ( 30) hydrogen bonds : bond 0.03074 ( 306) hydrogen bonds : angle 5.71468 ( 840) link_BETA1-4 : bond 0.00294 ( 3) link_BETA1-4 : angle 1.28861 ( 9) link_NAG-ASN : bond 0.00374 ( 5) link_NAG-ASN : angle 3.60488 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7136 (tpt) REVERT: A 154 GLU cc_start: 0.7646 (tt0) cc_final: 0.7392 (tt0) REVERT: A 165 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: A 187 LEU cc_start: 0.8504 (mm) cc_final: 0.8031 (mt) REVERT: A 230 ASN cc_start: 0.7288 (m-40) cc_final: 0.6812 (m110) REVERT: B 290 GLU cc_start: 0.5908 (tm-30) cc_final: 0.5590 (tm-30) REVERT: B 292 ASN cc_start: 0.7635 (t0) cc_final: 0.7263 (m-40) REVERT: B 303 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8099 (tpp-160) REVERT: C 39 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6956 (tm-30) REVERT: D 362 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7345 (mt-10) REVERT: E 60 ASN cc_start: 0.9032 (t0) cc_final: 0.8716 (t0) REVERT: E 78 HIS cc_start: 0.7962 (t-90) cc_final: 0.7113 (t-90) REVERT: E 80 ASP cc_start: 0.6525 (m-30) cc_final: 0.6003 (m-30) REVERT: E 83 ASP cc_start: 0.8864 (t70) cc_final: 0.8257 (t70) REVERT: E 85 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7899 (mp10) REVERT: E 114 MET cc_start: 0.5256 (tmt) cc_final: 0.5023 (tmt) REVERT: E 187 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7875 (mpp) REVERT: E 235 GLN cc_start: 0.6152 (pt0) cc_final: 0.5411 (tm-30) REVERT: F 90 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7886 (t0) REVERT: G 32 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8281 (pp30) REVERT: G 102 MET cc_start: 0.8504 (mpp) cc_final: 0.8239 (mtp) REVERT: G 109 ASP cc_start: 0.8044 (m-30) cc_final: 0.7637 (m-30) REVERT: H 92 ASP cc_start: 0.6799 (t0) cc_final: 0.6549 (t0) REVERT: H 99 TYR cc_start: 0.7724 (m-80) cc_final: 0.7117 (m-80) REVERT: H 119 LEU cc_start: 0.8595 (mm) cc_final: 0.8316 (mm) REVERT: I 35 GLN cc_start: 0.7965 (pt0) cc_final: 0.7192 (pm20) REVERT: I 91 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7077 (tm) outliers start: 35 outliers final: 24 residues processed: 227 average time/residue: 0.4357 time to fit residues: 110.1840 Evaluate side-chains 227 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LYS Chi-restraints excluded: chain I residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 95 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 146 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS E 279 GLN H 101 GLN H 104 ASN I 58 GLN I 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.175198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124627 restraints weight = 17340.358| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.55 r_work: 0.3655 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12640 Z= 0.120 Angle : 0.661 12.002 17202 Z= 0.314 Chirality : 0.042 0.147 1961 Planarity : 0.004 0.059 2203 Dihedral : 5.261 54.416 1882 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.67 % Allowed : 21.78 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.22), residues: 1556 helix: -0.11 (0.44), residues: 142 sheet: -0.56 (0.24), residues: 483 loop : -0.82 (0.21), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 180 TYR 0.023 0.001 TYR F 70 PHE 0.010 0.001 PHE D 321 TRP 0.049 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00289 (12617) covalent geometry : angle 0.65176 (17148) SS BOND : bond 0.00254 ( 15) SS BOND : angle 0.87455 ( 30) hydrogen bonds : bond 0.03110 ( 306) hydrogen bonds : angle 5.63473 ( 840) link_BETA1-4 : bond 0.00400 ( 3) link_BETA1-4 : angle 1.29823 ( 9) link_NAG-ASN : bond 0.00352 ( 5) link_NAG-ASN : angle 3.57135 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7145 (tpt) REVERT: A 154 GLU cc_start: 0.7653 (tt0) cc_final: 0.7404 (tt0) REVERT: A 165 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: A 174 TYR cc_start: 0.7796 (m-10) cc_final: 0.7543 (m-10) REVERT: A 187 LEU cc_start: 0.8510 (mm) cc_final: 0.8042 (mt) REVERT: A 230 ASN cc_start: 0.7327 (m-40) cc_final: 0.6852 (m110) REVERT: B 290 GLU cc_start: 0.5877 (tm-30) cc_final: 0.5544 (tm-30) REVERT: B 292 ASN cc_start: 0.7528 (t0) cc_final: 0.7144 (m-40) REVERT: B 303 ARG cc_start: 0.8391 (mmm160) cc_final: 0.8078 (tpp-160) REVERT: D 362 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7389 (mt-10) REVERT: E 60 ASN cc_start: 0.9029 (t0) cc_final: 0.8710 (t0) REVERT: E 78 HIS cc_start: 0.7892 (t-90) cc_final: 0.7100 (t-90) REVERT: E 83 ASP cc_start: 0.8835 (t70) cc_final: 0.8241 (t70) REVERT: E 85 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7914 (mp10) REVERT: E 114 MET cc_start: 0.5179 (tmt) cc_final: 0.4865 (tmt) REVERT: E 187 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: E 235 GLN cc_start: 0.6113 (pt0) cc_final: 0.5356 (tm-30) REVERT: E 451 MET cc_start: 0.4501 (ppp) cc_final: 0.2820 (tpt) REVERT: F 90 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7961 (t0) REVERT: G 32 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8297 (pp30) REVERT: G 79 TYR cc_start: 0.8187 (m-80) cc_final: 0.7981 (m-10) REVERT: G 102 MET cc_start: 0.8474 (mpp) cc_final: 0.8244 (mtp) REVERT: G 109 ASP cc_start: 0.7937 (m-30) cc_final: 0.7537 (m-30) REVERT: G 135 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7762 (tm-30) REVERT: H 92 ASP cc_start: 0.6793 (t0) cc_final: 0.6557 (t0) REVERT: H 99 TYR cc_start: 0.7733 (m-80) cc_final: 0.7161 (m-80) REVERT: H 119 LEU cc_start: 0.8618 (mm) cc_final: 0.8342 (mm) REVERT: I 35 GLN cc_start: 0.7941 (pt0) cc_final: 0.7176 (pm20) REVERT: I 91 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7060 (tm) outliers start: 36 outliers final: 22 residues processed: 231 average time/residue: 0.4374 time to fit residues: 112.7435 Evaluate side-chains 231 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 100 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.0870 chunk 61 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS E 199 HIS E 279 GLN H 101 GLN H 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.173940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122767 restraints weight = 17552.476| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.60 r_work: 0.3650 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12640 Z= 0.145 Angle : 0.667 11.332 17202 Z= 0.319 Chirality : 0.042 0.158 1961 Planarity : 0.004 0.061 2203 Dihedral : 5.314 54.602 1882 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.59 % Allowed : 22.22 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.22), residues: 1556 helix: -0.19 (0.43), residues: 142 sheet: -0.46 (0.25), residues: 455 loop : -0.90 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 180 TYR 0.022 0.002 TYR F 70 PHE 0.009 0.001 PHE H 87 TRP 0.042 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 Details of bonding type rmsd covalent geometry : bond 0.00352 (12617) covalent geometry : angle 0.65768 (17148) SS BOND : bond 0.00282 ( 15) SS BOND : angle 0.99588 ( 30) hydrogen bonds : bond 0.03219 ( 306) hydrogen bonds : angle 5.65422 ( 840) link_BETA1-4 : bond 0.00259 ( 3) link_BETA1-4 : angle 1.32367 ( 9) link_NAG-ASN : bond 0.00349 ( 5) link_NAG-ASN : angle 3.55002 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7070 (tpt) REVERT: A 154 GLU cc_start: 0.7665 (tt0) cc_final: 0.7403 (tt0) REVERT: A 165 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: A 187 LEU cc_start: 0.8554 (mm) cc_final: 0.8086 (mt) REVERT: A 230 ASN cc_start: 0.7341 (m-40) cc_final: 0.6896 (m110) REVERT: A 231 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7975 (tptm) REVERT: B 290 GLU cc_start: 0.5911 (tm-30) cc_final: 0.5625 (tm-30) REVERT: B 292 ASN cc_start: 0.7567 (t0) cc_final: 0.7142 (OUTLIER) REVERT: C 113 MET cc_start: 0.8674 (ttp) cc_final: 0.8464 (ttm) REVERT: C 255 ARG cc_start: 0.8581 (ptt90) cc_final: 0.8355 (ptt-90) REVERT: D 362 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7430 (mt-10) REVERT: E 60 ASN cc_start: 0.9047 (t0) cc_final: 0.8723 (t0) REVERT: E 78 HIS cc_start: 0.8173 (t70) cc_final: 0.7349 (t-90) REVERT: E 83 ASP cc_start: 0.8858 (t70) cc_final: 0.8243 (t70) REVERT: E 85 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7924 (mp10) REVERT: E 114 MET cc_start: 0.5287 (tmt) cc_final: 0.5017 (tmt) REVERT: E 187 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: E 235 GLN cc_start: 0.6182 (pt0) cc_final: 0.5421 (tm-30) REVERT: E 451 MET cc_start: 0.4505 (ppp) cc_final: 0.2793 (tpt) REVERT: F 90 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7937 (t0) REVERT: G 32 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8280 (pp30) REVERT: G 102 MET cc_start: 0.8495 (mpp) cc_final: 0.8267 (mtp) REVERT: G 109 ASP cc_start: 0.8030 (m-30) cc_final: 0.7579 (m-30) REVERT: G 135 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7814 (tm-30) REVERT: H 99 TYR cc_start: 0.7775 (m-80) cc_final: 0.7243 (m-80) REVERT: I 35 GLN cc_start: 0.7970 (pt0) cc_final: 0.7300 (pm20) REVERT: I 91 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7065 (tm) outliers start: 35 outliers final: 28 residues processed: 226 average time/residue: 0.4715 time to fit residues: 118.2445 Evaluate side-chains 233 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 382 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 187 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 96 optimal weight: 50.0000 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS E 279 GLN H 101 GLN H 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.173870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123215 restraints weight = 17341.787| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.47 r_work: 0.3650 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12640 Z= 0.139 Angle : 0.668 10.666 17202 Z= 0.320 Chirality : 0.042 0.163 1961 Planarity : 0.005 0.064 2203 Dihedral : 5.308 54.416 1882 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.96 % Allowed : 22.22 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.22), residues: 1556 helix: -0.27 (0.44), residues: 136 sheet: -0.46 (0.24), residues: 461 loop : -0.86 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 303 TYR 0.021 0.002 TYR A 81 PHE 0.009 0.001 PHE H 87 TRP 0.039 0.001 TRP H 55 HIS 0.006 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00334 (12617) covalent geometry : angle 0.65910 (17148) SS BOND : bond 0.00272 ( 15) SS BOND : angle 0.98290 ( 30) hydrogen bonds : bond 0.03193 ( 306) hydrogen bonds : angle 5.64430 ( 840) link_BETA1-4 : bond 0.00258 ( 3) link_BETA1-4 : angle 1.34550 ( 9) link_NAG-ASN : bond 0.00344 ( 5) link_NAG-ASN : angle 3.52649 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6194.45 seconds wall clock time: 106 minutes 8.92 seconds (6368.92 seconds total)