Starting phenix.real_space_refine on Wed Jul 30 13:31:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rex_19111/07_2025/8rex_19111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rex_19111/07_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_19111/07_2025/8rex_19111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rex_19111/07_2025/8rex_19111.map" model { file = "/net/cci-nas-00/data/ceres_data/8rex_19111/07_2025/8rex_19111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rex_19111/07_2025/8rex_19111.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.57, per 1000 atoms: 0.69 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.71 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: 3.97 Time building geometry restraints manager: 3.21 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: 7.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.700 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:15.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (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 TRP 0.037 0.002 TRP D 330 HIS 0.008 0.001 HIS E 182 PHE 0.012 0.001 PHE H 87 TYR 0.030 0.002 TYR G 79 ARG 0.013 0.001 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 5) link_NAG-ASN : angle 3.59079 ( 15) link_BETA1-4 : bond 0.00431 ( 3) link_BETA1-4 : angle 1.45175 ( 9) hydrogen bonds : bond 0.25792 ( 306) hydrogen bonds : angle 10.06101 ( 840) SS BOND : bond 0.00246 ( 15) SS BOND : angle 1.25459 ( 30) covalent geometry : bond 0.00435 (12617) covalent geometry : angle 0.83013 (17148) *********************** 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 : 1.602 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: 1.0632 time to fit residues: 320.2056 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 : 1.307 ------------------------------------------------------------------------------- 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 130 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.174321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.122735 restraints weight = 17392.734| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.60 r_work: 0.3624 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12640 Z= 0.187 Angle : 0.697 11.807 17202 Z= 0.345 Chirality : 0.044 0.160 1961 Planarity : 0.005 0.049 2203 Dihedral : 6.486 55.449 1886 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.89 % Allowed : 12.15 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (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 TRP 0.018 0.002 TRP H 55 HIS 0.006 0.001 HIS E 182 PHE 0.017 0.002 PHE H 87 TYR 0.024 0.002 TYR F 112 ARG 0.007 0.001 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 5) link_NAG-ASN : angle 3.76037 ( 15) link_BETA1-4 : bond 0.00177 ( 3) link_BETA1-4 : angle 1.43072 ( 9) hydrogen bonds : bond 0.04374 ( 306) hydrogen bonds : angle 7.23429 ( 840) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.37177 ( 30) covalent geometry : bond 0.00450 (12617) covalent geometry : angle 0.68589 (17148) *********************** 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 261 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.366 Fit side-chains REVERT: A 180 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7826 (ptm-80) REVERT: A 230 ASN cc_start: 0.7383 (m-40) cc_final: 0.6796 (m-40) REVERT: B 303 ARG cc_start: 0.8574 (mmm160) cc_final: 0.8242 (tpp-160) REVERT: B 313 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: C 39 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6966 (tm-30) REVERT: C 173 LYS cc_start: 0.7448 (tmtt) cc_final: 0.7184 (tmtt) REVERT: C 254 ASN cc_start: 0.5303 (t0) cc_final: 0.5071 (t0) REVERT: E 80 ASP cc_start: 0.6562 (m-30) cc_final: 0.5986 (m-30) REVERT: E 83 ASP cc_start: 0.8883 (t70) cc_final: 0.8580 (t70) REVERT: E 235 GLN cc_start: 0.6213 (pt0) cc_final: 0.5654 (tm-30) REVERT: E 349 ARG cc_start: 0.5477 (tmm160) cc_final: 0.5123 (tmt170) REVERT: F 90 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8122 (t0) REVERT: G 54 TYR cc_start: 0.7899 (m-80) cc_final: 0.7692 (m-80) REVERT: G 109 ASP cc_start: 0.8281 (m-30) cc_final: 0.7990 (m-30) REVERT: G 135 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7831 (tm-30) REVERT: H 22 GLN cc_start: 0.7880 (pm20) cc_final: 0.7228 (pp30) REVERT: H 55 TRP cc_start: 0.8783 (m100) cc_final: 0.8534 (m100) REVERT: H 99 TYR cc_start: 0.7623 (m-80) cc_final: 0.7006 (m-80) outliers start: 39 outliers final: 17 residues processed: 239 average time/residue: 1.1066 time to fit residues: 291.2515 Evaluate side-chains 222 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 D residue 383 ILE Chi-restraints excluded: chain E residue 86 ILE 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 112 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 E 78 HIS E 199 HIS 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 = 0.4377 r_free = 0.4377 target = 0.172063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.121077 restraints weight = 17632.583| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.54 r_work: 0.3604 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12640 Z= 0.185 Angle : 0.669 11.145 17202 Z= 0.329 Chirality : 0.043 0.147 1961 Planarity : 0.005 0.049 2203 Dihedral : 6.156 55.439 1882 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.63 % Allowed : 15.63 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1556 helix: -0.79 (0.42), residues: 142 sheet: -0.69 (0.25), residues: 441 loop : -1.19 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 55 HIS 0.007 0.001 HIS E 182 PHE 0.009 0.001 PHE C 134 TYR 0.022 0.002 TYR G 124 ARG 0.010 0.001 ARG F 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 5) link_NAG-ASN : angle 3.73399 ( 15) link_BETA1-4 : bond 0.00100 ( 3) link_BETA1-4 : angle 1.37514 ( 9) hydrogen bonds : bond 0.04027 ( 306) hydrogen bonds : angle 6.66201 ( 840) SS BOND : bond 0.00352 ( 15) SS BOND : angle 1.29752 ( 30) covalent geometry : bond 0.00442 (12617) covalent geometry : angle 0.65826 (17148) *********************** 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 256 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 1.377 Fit side-chains REVERT: A 154 GLU cc_start: 0.7759 (tt0) cc_final: 0.7546 (tt0) REVERT: A 165 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7521 (tp30) REVERT: A 174 TYR cc_start: 0.7839 (m-10) cc_final: 0.7606 (m-10) REVERT: A 180 ARG cc_start: 0.8127 (ptm-80) cc_final: 0.7786 (ptm-80) REVERT: A 230 ASN cc_start: 0.7318 (m-40) cc_final: 0.6862 (m110) REVERT: A 231 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7952 (tptm) REVERT: B 290 GLU cc_start: 0.6146 (tm-30) cc_final: 0.5637 (tm-30) REVERT: B 303 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8266 (tpp-160) REVERT: B 304 LYS cc_start: 0.8781 (pttt) cc_final: 0.8528 (pmtt) REVERT: B 313 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: C 39 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7159 (tm-30) REVERT: C 173 LYS cc_start: 0.7482 (tmtt) cc_final: 0.7207 (tmtt) REVERT: C 254 ASN cc_start: 0.5477 (t0) cc_final: 0.5245 (t0) REVERT: E 78 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7086 (t70) REVERT: E 80 ASP cc_start: 0.6566 (m-30) cc_final: 0.5651 (m-30) REVERT: E 83 ASP cc_start: 0.8881 (t70) cc_final: 0.8493 (t70) REVERT: E 85 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8097 (mp10) REVERT: E 187 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7931 (mpp) REVERT: E 235 GLN cc_start: 0.6200 (pt0) cc_final: 0.5541 (tm-30) REVERT: E 349 ARG cc_start: 0.5597 (OUTLIER) cc_final: 0.4691 (mmm160) REVERT: F 90 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8072 (t0) REVERT: F 100 GLN cc_start: 0.8834 (mp10) cc_final: 0.8626 (mp10) REVERT: G 53 MET cc_start: 0.7180 (mmp) cc_final: 0.6816 (mmp) REVERT: G 109 ASP cc_start: 0.8312 (m-30) cc_final: 0.7982 (m-30) REVERT: G 135 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7839 (tm-30) REVERT: H 22 GLN cc_start: 0.7877 (pm20) cc_final: 0.7263 (pp30) REVERT: H 99 TYR cc_start: 0.7686 (m-80) cc_final: 0.7123 (m-80) REVERT: H 102 MET cc_start: 0.7592 (mpp) cc_final: 0.7365 (mpt) REVERT: I 91 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7228 (tm) outliers start: 49 outliers final: 24 residues processed: 228 average time/residue: 0.9683 time to fit residues: 244.6006 Evaluate side-chains 229 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain B residue 323 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 330 LEU Chi-restraints excluded: chain E residue 349 ARG 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 G residue 44 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 24 VAL Chi-restraints excluded: chain H residue 67 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 48 optimal weight: 4.9990 chunk 49 optimal weight: 0.1980 chunk 149 optimal weight: 0.0980 chunk 125 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 345 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 = 0.174898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.124821 restraints weight = 17481.541| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.73 r_work: 0.3645 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2092 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= 0.121 Angle : 0.617 11.054 17202 Z= 0.302 Chirality : 0.041 0.152 1961 Planarity : 0.004 0.048 2203 Dihedral : 5.893 54.899 1882 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.04 % Allowed : 17.70 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1556 helix: -0.44 (0.43), residues: 142 sheet: -0.56 (0.25), residues: 433 loop : -1.13 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 78 HIS 0.007 0.001 HIS C 167 PHE 0.013 0.001 PHE H 87 TYR 0.029 0.001 TYR F 70 ARG 0.008 0.000 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 3.69200 ( 15) link_BETA1-4 : bond 0.00234 ( 3) link_BETA1-4 : angle 1.28354 ( 9) hydrogen bonds : bond 0.03479 ( 306) hydrogen bonds : angle 6.32720 ( 840) SS BOND : bond 0.00285 ( 15) SS BOND : angle 1.05328 ( 30) covalent geometry : bond 0.00285 (12617) covalent geometry : angle 0.60569 (17148) *********************** 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 262 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 1.433 Fit side-chains REVERT: A 165 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: A 180 ARG cc_start: 0.8071 (ptm-80) cc_final: 0.7818 (ptm-80) REVERT: A 230 ASN cc_start: 0.7269 (m-40) cc_final: 0.6808 (m110) REVERT: B 290 GLU cc_start: 0.6013 (tm-30) cc_final: 0.5563 (tm-30) REVERT: B 303 ARG cc_start: 0.8534 (mmm160) cc_final: 0.8214 (tpp-160) REVERT: C 39 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7094 (tm-30) REVERT: C 83 SER cc_start: 0.8008 (m) cc_final: 0.7776 (p) REVERT: C 173 LYS cc_start: 0.7488 (tmtt) cc_final: 0.7173 (tmtt) REVERT: D 301 ASP cc_start: 0.7716 (t0) cc_final: 0.7443 (t0) REVERT: E 78 HIS cc_start: 0.7593 (OUTLIER) cc_final: 0.6703 (t-90) REVERT: E 80 ASP cc_start: 0.6663 (m-30) cc_final: 0.5185 (m-30) REVERT: E 83 ASP cc_start: 0.8924 (t70) cc_final: 0.8484 (t70) REVERT: E 85 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7894 (mp10) REVERT: E 187 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7892 (mpp) REVERT: E 235 GLN cc_start: 0.6154 (pt0) cc_final: 0.5480 (tm-30) REVERT: E 349 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.4879 (mmm160) REVERT: F 90 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8070 (t0) REVERT: G 32 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8607 (pp30) REVERT: G 33 PRO cc_start: 0.9347 (Cg_endo) cc_final: 0.9001 (Cg_exo) REVERT: G 39 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8554 (mp) REVERT: G 53 MET cc_start: 0.7210 (mmp) cc_final: 0.6859 (mmp) REVERT: G 68 SER cc_start: 0.8637 (t) cc_final: 0.8399 (m) REVERT: G 109 ASP cc_start: 0.8175 (m-30) cc_final: 0.7803 (m-30) REVERT: G 135 GLN cc_start: 0.8278 (tp-100) cc_final: 0.7811 (tm-30) REVERT: H 22 GLN cc_start: 0.7844 (pm20) cc_final: 0.7269 (pp30) REVERT: H 99 TYR cc_start: 0.7672 (m-80) cc_final: 0.7143 (m-80) REVERT: I 91 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7180 (tm) outliers start: 41 outliers final: 20 residues processed: 240 average time/residue: 1.3350 time to fit residues: 358.8584 Evaluate side-chains 233 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 3.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU 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 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 349 ARG 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 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 39 LEU Chi-restraints excluded: chain G residue 40 SER 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 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 142 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 61 GLN E 78 HIS E 199 HIS H 101 GLN H 104 ASN I 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.172514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121545 restraints weight = 17442.482| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.75 r_work: 0.3603 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12640 Z= 0.165 Angle : 0.651 11.019 17202 Z= 0.317 Chirality : 0.042 0.142 1961 Planarity : 0.005 0.049 2203 Dihedral : 5.897 59.664 1882 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.48 % Allowed : 18.89 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1556 helix: -0.42 (0.43), residues: 142 sheet: -0.62 (0.25), residues: 427 loop : -1.13 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 55 HIS 0.006 0.001 HIS E 182 PHE 0.011 0.001 PHE H 87 TYR 0.019 0.002 TYR G 124 ARG 0.012 0.001 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 5) link_NAG-ASN : angle 3.71227 ( 15) link_BETA1-4 : bond 0.00128 ( 3) link_BETA1-4 : angle 1.33021 ( 9) hydrogen bonds : bond 0.03542 ( 306) hydrogen bonds : angle 6.13720 ( 840) SS BOND : bond 0.00342 ( 15) SS BOND : angle 1.30075 ( 30) covalent geometry : bond 0.00399 (12617) covalent geometry : angle 0.63976 (17148) *********************** 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 259 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: A 180 ARG cc_start: 0.8112 (ptm-80) cc_final: 0.7911 (ptm-80) REVERT: A 230 ASN cc_start: 0.7322 (m-40) cc_final: 0.6853 (m110) REVERT: A 231 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7968 (tptm) REVERT: B 290 GLU cc_start: 0.6109 (tm-30) cc_final: 0.5656 (tm-30) REVERT: E 78 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7148 (t70) REVERT: E 80 ASP cc_start: 0.6781 (m-30) cc_final: 0.5585 (m-30) REVERT: E 83 ASP cc_start: 0.8883 (t70) cc_final: 0.8423 (t70) REVERT: E 85 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8118 (mp10) REVERT: E 187 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7946 (mpp) REVERT: E 235 GLN cc_start: 0.6144 (pt0) cc_final: 0.5453 (tm-30) REVERT: E 349 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.4821 (mmm160) REVERT: E 451 MET cc_start: 0.4707 (ppp) cc_final: 0.3139 (tpt) REVERT: F 90 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7963 (t0) REVERT: G 32 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8514 (pp30) REVERT: G 33 PRO cc_start: 0.9376 (Cg_endo) cc_final: 0.9005 (Cg_exo) REVERT: G 39 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8540 (mp) REVERT: G 53 MET cc_start: 0.7289 (mmp) cc_final: 0.6857 (mmp) REVERT: G 109 ASP cc_start: 0.8210 (m-30) cc_final: 0.7839 (m-30) REVERT: G 135 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7893 (tm-30) REVERT: H 22 GLN cc_start: 0.7821 (pm20) cc_final: 0.7246 (pp30) REVERT: H 99 TYR cc_start: 0.7737 (m-80) cc_final: 0.7243 (m-80) REVERT: I 91 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7163 (tm) outliers start: 47 outliers final: 24 residues processed: 233 average time/residue: 0.9482 time to fit residues: 245.9559 Evaluate side-chains 239 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 B residue 331 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 349 ARG 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 G residue 26 SER Chi-restraints excluded: chain G residue 39 LEU 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 I residue 91 LEU Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 5 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 115 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 13 optimal weight: 0.1980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 102 HIS 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 = 0.4410 r_free = 0.4410 target = 0.175110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.124785 restraints weight = 17576.475| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.54 r_work: 0.3655 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12640 Z= 0.110 Angle : 0.624 10.856 17202 Z= 0.302 Chirality : 0.041 0.147 1961 Planarity : 0.004 0.049 2203 Dihedral : 5.696 58.261 1882 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.96 % Allowed : 20.07 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1556 helix: -0.23 (0.44), residues: 142 sheet: -0.61 (0.24), residues: 456 loop : -0.98 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 55 HIS 0.008 0.001 HIS E 78 PHE 0.010 0.001 PHE D 321 TYR 0.024 0.001 TYR F 70 ARG 0.014 0.001 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 5) link_NAG-ASN : angle 3.64746 ( 15) link_BETA1-4 : bond 0.00298 ( 3) link_BETA1-4 : angle 1.25463 ( 9) hydrogen bonds : bond 0.03182 ( 306) hydrogen bonds : angle 5.94618 ( 840) SS BOND : bond 0.00251 ( 15) SS BOND : angle 0.97507 ( 30) covalent geometry : bond 0.00260 (12617) covalent geometry : angle 0.61393 (17148) *********************** 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 263 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 187 LEU cc_start: 0.8583 (mm) cc_final: 0.8144 (mt) REVERT: A 230 ASN cc_start: 0.7276 (m-40) cc_final: 0.6800 (m110) REVERT: B 290 GLU cc_start: 0.6004 (tm-30) cc_final: 0.5640 (tm-30) REVERT: B 303 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8179 (tpp-160) REVERT: C 39 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7043 (tm-30) REVERT: E 78 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6813 (t-90) REVERT: E 80 ASP cc_start: 0.6782 (m-30) cc_final: 0.5122 (m-30) REVERT: E 83 ASP cc_start: 0.8859 (t70) cc_final: 0.8260 (t70) REVERT: E 85 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7928 (mp10) REVERT: E 187 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: E 235 GLN cc_start: 0.6133 (pt0) cc_final: 0.5424 (tm-30) REVERT: E 349 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.4824 (mmm160) REVERT: E 451 MET cc_start: 0.4827 (ppp) cc_final: 0.3297 (tpt) REVERT: F 90 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7973 (t0) REVERT: G 109 ASP cc_start: 0.8119 (m-30) cc_final: 0.7717 (m-30) REVERT: G 135 GLN cc_start: 0.8299 (tp-100) cc_final: 0.7847 (tm-30) REVERT: H 22 GLN cc_start: 0.7797 (pm20) cc_final: 0.7264 (pp30) REVERT: H 99 TYR cc_start: 0.7724 (m-80) cc_final: 0.7211 (m-80) REVERT: H 119 LEU cc_start: 0.8630 (mm) cc_final: 0.8335 (mm) REVERT: I 29 MET cc_start: 0.6355 (tmm) cc_final: 0.6142 (tmt) REVERT: I 35 GLN cc_start: 0.8004 (pt0) cc_final: 0.7270 (pm20) REVERT: I 91 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7135 (tm) outliers start: 40 outliers final: 20 residues processed: 244 average time/residue: 1.0072 time to fit residues: 277.3426 Evaluate side-chains 236 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 203 VAL 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 78 HIS Chi-restraints excluded: chain E residue 86 ILE 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 273 VAL Chi-restraints excluded: chain E residue 349 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 107 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 22 optimal weight: 0.0370 chunk 109 optimal weight: 10.0000 chunk 119 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 G 104 ASN H 101 GLN H 104 ASN I 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.174510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.122973 restraints weight = 17482.788| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.75 r_work: 0.3631 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2552 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= 0.129 Angle : 0.642 11.754 17202 Z= 0.309 Chirality : 0.041 0.144 1961 Planarity : 0.004 0.050 2203 Dihedral : 5.570 54.613 1882 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.19 % Allowed : 20.37 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1556 helix: -0.14 (0.44), residues: 142 sheet: -0.65 (0.24), residues: 463 loop : -0.89 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 PHE 0.010 0.001 PHE H 87 TYR 0.023 0.001 TYR F 70 ARG 0.012 0.001 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 5) link_NAG-ASN : angle 3.66330 ( 15) link_BETA1-4 : bond 0.00255 ( 3) link_BETA1-4 : angle 1.27029 ( 9) hydrogen bonds : bond 0.03220 ( 306) hydrogen bonds : angle 5.87961 ( 840) SS BOND : bond 0.00310 ( 15) SS BOND : angle 1.11356 ( 30) covalent geometry : bond 0.00311 (12617) covalent geometry : angle 0.63105 (17148) *********************** 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 258 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7527 (tpt) cc_final: 0.6915 (tpt) REVERT: A 165 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: A 174 TYR cc_start: 0.7796 (m-10) cc_final: 0.7565 (m-10) REVERT: A 187 LEU cc_start: 0.8564 (mm) cc_final: 0.8101 (mt) REVERT: A 230 ASN cc_start: 0.7269 (m-40) cc_final: 0.6832 (m110) REVERT: A 231 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7944 (tptm) REVERT: B 290 GLU cc_start: 0.5954 (tm-30) cc_final: 0.5623 (tm-30) REVERT: B 303 ARG cc_start: 0.8473 (mmm160) cc_final: 0.8150 (tpp-160) REVERT: C 78 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8132 (mt) REVERT: E 60 ASN cc_start: 0.9069 (t0) cc_final: 0.8762 (t0) REVERT: E 78 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6842 (t-170) REVERT: E 80 ASP cc_start: 0.6834 (m-30) cc_final: 0.5635 (m-30) REVERT: E 83 ASP cc_start: 0.8862 (t70) cc_final: 0.8264 (t70) REVERT: E 85 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7905 (mp10) REVERT: E 187 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7938 (mpp) REVERT: E 235 GLN cc_start: 0.6158 (pt0) cc_final: 0.5438 (tm-30) REVERT: E 349 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.4433 (mmm160) REVERT: E 451 MET cc_start: 0.4498 (ppp) cc_final: 0.3218 (tpt) REVERT: F 90 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7927 (t0) REVERT: G 32 GLN cc_start: 0.9082 (tp40) cc_final: 0.8356 (pp30) REVERT: G 109 ASP cc_start: 0.8051 (m-30) cc_final: 0.7681 (m-30) REVERT: G 135 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7852 (tm-30) REVERT: H 22 GLN cc_start: 0.7825 (pm20) cc_final: 0.7149 (pp30) REVERT: H 99 TYR cc_start: 0.7738 (m-80) cc_final: 0.7203 (m-80) REVERT: H 119 LEU cc_start: 0.8638 (mm) cc_final: 0.8414 (mm) REVERT: I 35 GLN cc_start: 0.8003 (pt0) cc_final: 0.7235 (pm20) REVERT: I 91 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7090 (tm) outliers start: 43 outliers final: 24 residues processed: 236 average time/residue: 0.9297 time to fit residues: 245.2021 Evaluate side-chains 240 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 B residue 292 ASN 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 39 LEU 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 264 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 389 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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 = 0.4394 r_free = 0.4394 target = 0.173383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122174 restraints weight = 17591.103| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.59 r_work: 0.3616 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12640 Z= 0.146 Angle : 0.659 10.808 17202 Z= 0.317 Chirality : 0.042 0.196 1961 Planarity : 0.004 0.056 2203 Dihedral : 5.527 54.692 1882 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.04 % Allowed : 21.48 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1556 helix: -0.13 (0.44), residues: 142 sheet: -0.67 (0.24), residues: 466 loop : -0.88 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 55 HIS 0.010 0.001 HIS E 78 PHE 0.009 0.001 PHE H 87 TYR 0.015 0.002 TYR F 112 ARG 0.013 0.001 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 5) link_NAG-ASN : angle 3.64015 ( 15) link_BETA1-4 : bond 0.00233 ( 3) link_BETA1-4 : angle 1.28448 ( 9) hydrogen bonds : bond 0.03299 ( 306) hydrogen bonds : angle 5.83217 ( 840) SS BOND : bond 0.00280 ( 15) SS BOND : angle 1.11552 ( 30) covalent geometry : bond 0.00353 (12617) covalent geometry : angle 0.64860 (17148) *********************** 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 254 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7262 (tpt) REVERT: A 165 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: A 187 LEU cc_start: 0.8587 (mm) cc_final: 0.8096 (mt) REVERT: A 230 ASN cc_start: 0.7262 (m-40) cc_final: 0.6818 (m110) REVERT: A 231 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7951 (tptm) REVERT: B 290 GLU cc_start: 0.5958 (tm-30) cc_final: 0.5647 (tm-30) REVERT: B 303 ARG cc_start: 0.8472 (mmm160) cc_final: 0.8169 (tpp-160) REVERT: C 78 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8165 (mt) REVERT: D 362 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7369 (mt-10) REVERT: E 60 ASN cc_start: 0.9047 (t0) cc_final: 0.8733 (t0) REVERT: E 78 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7262 (t70) REVERT: E 80 ASP cc_start: 0.6798 (m-30) cc_final: 0.5746 (m-30) REVERT: E 83 ASP cc_start: 0.8853 (t70) cc_final: 0.8242 (t70) REVERT: E 85 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7915 (mp10) REVERT: E 187 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7931 (mpp) REVERT: E 235 GLN cc_start: 0.6130 (pt0) cc_final: 0.5395 (tm-30) REVERT: E 349 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.4491 (mmm160) REVERT: F 90 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.7951 (t0) REVERT: G 32 GLN cc_start: 0.9107 (tp40) cc_final: 0.8303 (pp30) REVERT: G 53 MET cc_start: 0.7117 (mmp) cc_final: 0.6756 (mmp) REVERT: G 109 ASP cc_start: 0.8062 (m-30) cc_final: 0.7618 (m-30) REVERT: G 135 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7851 (tm-30) REVERT: H 99 TYR cc_start: 0.7767 (m-80) cc_final: 0.7216 (m-80) REVERT: I 35 GLN cc_start: 0.7938 (pt0) cc_final: 0.7222 (pm20) REVERT: I 91 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7085 (tm) outliers start: 41 outliers final: 28 residues processed: 233 average time/residue: 0.8823 time to fit residues: 230.1250 Evaluate side-chains 240 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 B residue 292 ASN 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 D residue 383 ILE Chi-restraints excluded: chain E residue 39 LEU 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 264 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 389 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 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 Chi-restraints excluded: chain I residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 102 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 115 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 H 101 GLN H 104 ASN I 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.173187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122011 restraints weight = 17500.088| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.60 r_work: 0.3619 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12640 Z= 0.148 Angle : 0.678 11.177 17202 Z= 0.326 Chirality : 0.042 0.146 1961 Planarity : 0.004 0.059 2203 Dihedral : 5.465 54.741 1882 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.19 % Allowed : 21.93 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1556 helix: -0.17 (0.44), residues: 136 sheet: -0.64 (0.24), residues: 467 loop : -0.86 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 55 HIS 0.008 0.001 HIS E 78 PHE 0.009 0.001 PHE H 87 TYR 0.035 0.002 TYR F 70 ARG 0.014 0.001 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 3.61765 ( 15) link_BETA1-4 : bond 0.00240 ( 3) link_BETA1-4 : angle 1.27933 ( 9) hydrogen bonds : bond 0.03290 ( 306) hydrogen bonds : angle 5.82873 ( 840) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.25411 ( 30) covalent geometry : bond 0.00357 (12617) covalent geometry : angle 0.66823 (17148) *********************** 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 248 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7247 (tpt) REVERT: A 165 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: A 187 LEU cc_start: 0.8598 (mm) cc_final: 0.8100 (mt) REVERT: A 230 ASN cc_start: 0.7284 (m-40) cc_final: 0.6838 (m110) REVERT: A 231 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7968 (tptm) REVERT: B 290 GLU cc_start: 0.5946 (tm-30) cc_final: 0.5645 (tm-30) REVERT: B 303 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8153 (tpp-160) REVERT: D 362 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7368 (mt-10) REVERT: E 60 ASN cc_start: 0.9060 (t0) cc_final: 0.8743 (t0) REVERT: E 83 ASP cc_start: 0.8852 (t70) cc_final: 0.8229 (t70) REVERT: E 85 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7940 (mp10) REVERT: E 187 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7944 (mpp) REVERT: E 235 GLN cc_start: 0.6183 (pt0) cc_final: 0.5399 (tm-30) REVERT: E 349 ARG cc_start: 0.5642 (OUTLIER) cc_final: 0.4389 (mmm160) REVERT: E 451 MET cc_start: 0.4346 (ppp) cc_final: 0.2692 (tpt) REVERT: F 90 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7979 (t0) REVERT: G 53 MET cc_start: 0.7158 (mmp) cc_final: 0.6865 (mmp) REVERT: G 109 ASP cc_start: 0.8075 (m-30) cc_final: 0.7615 (m-30) REVERT: G 135 GLN cc_start: 0.8281 (tp-100) cc_final: 0.7844 (tm-30) REVERT: H 99 TYR cc_start: 0.7785 (m-80) cc_final: 0.7247 (m-80) REVERT: I 35 GLN cc_start: 0.8000 (pt0) cc_final: 0.7265 (pm20) REVERT: I 91 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7104 (tm) outliers start: 43 outliers final: 27 residues processed: 227 average time/residue: 1.2564 time to fit residues: 319.7828 Evaluate side-chains 234 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 B residue 292 ASN 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 D residue 383 ILE 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 264 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 389 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 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 20 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 95 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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 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 = 0.4385 r_free = 0.4385 target = 0.172631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121642 restraints weight = 17513.564| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.59 r_work: 0.3621 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12640 Z= 0.154 Angle : 0.682 10.770 17202 Z= 0.328 Chirality : 0.043 0.171 1961 Planarity : 0.004 0.062 2203 Dihedral : 5.431 54.719 1882 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.96 % Allowed : 22.37 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1556 helix: -0.26 (0.44), residues: 136 sheet: -0.58 (0.25), residues: 447 loop : -0.96 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 PHE 0.010 0.001 PHE H 87 TYR 0.023 0.002 TYR F 70 ARG 0.014 0.001 ARG C 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 5) link_NAG-ASN : angle 3.62268 ( 15) link_BETA1-4 : bond 0.00270 ( 3) link_BETA1-4 : angle 1.30314 ( 9) hydrogen bonds : bond 0.03319 ( 306) hydrogen bonds : angle 5.81038 ( 840) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.20693 ( 30) covalent geometry : bond 0.00371 (12617) covalent geometry : angle 0.67216 (17148) ********************** 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 251 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7288 (tpt) REVERT: A 165 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: A 187 LEU cc_start: 0.8633 (mm) cc_final: 0.8186 (mt) REVERT: A 230 ASN cc_start: 0.7314 (m-40) cc_final: 0.6885 (m110) REVERT: A 231 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7973 (tptm) REVERT: B 303 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8194 (tpp-160) REVERT: D 362 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7376 (mt-10) REVERT: E 60 ASN cc_start: 0.9070 (t0) cc_final: 0.8753 (t0) REVERT: E 83 ASP cc_start: 0.8871 (t70) cc_final: 0.8279 (t70) REVERT: E 85 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7942 (mp10) REVERT: E 187 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7945 (mpp) REVERT: E 235 GLN cc_start: 0.6140 (pt0) cc_final: 0.5371 (tm-30) REVERT: E 349 ARG cc_start: 0.5757 (OUTLIER) cc_final: 0.4427 (mmm160) REVERT: E 366 LEU cc_start: 0.4065 (OUTLIER) cc_final: 0.3802 (mp) REVERT: E 451 MET cc_start: 0.4455 (ppp) cc_final: 0.2756 (tpt) REVERT: F 90 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7980 (t0) REVERT: G 32 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8341 (pp30) REVERT: G 53 MET cc_start: 0.7288 (mmp) cc_final: 0.7002 (mmp) REVERT: G 109 ASP cc_start: 0.8109 (m-30) cc_final: 0.7709 (m-30) REVERT: G 135 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7828 (tm-30) REVERT: G 138 VAL cc_start: 0.7724 (t) cc_final: 0.7452 (p) REVERT: H 99 TYR cc_start: 0.7854 (m-80) cc_final: 0.7303 (m-80) REVERT: I 35 GLN cc_start: 0.7991 (pt0) cc_final: 0.7258 (pm20) REVERT: I 91 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7106 (tm) outliers start: 40 outliers final: 29 residues processed: 230 average time/residue: 1.0031 time to fit residues: 257.7953 Evaluate side-chains 244 residues out of total 1367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 B residue 292 ASN 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 D residue 383 ILE 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 264 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 349 ARG Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 389 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 153 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS G 104 ASN 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 = 0.4400 r_free = 0.4400 target = 0.174141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.123141 restraints weight = 17555.162| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.63 r_work: 0.3644 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12640 Z= 0.127 Angle : 0.674 11.008 17202 Z= 0.326 Chirality : 0.042 0.157 1961 Planarity : 0.005 0.062 2203 Dihedral : 5.402 54.381 1882 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.89 % Allowed : 22.81 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1556 helix: -0.21 (0.44), residues: 136 sheet: -0.60 (0.24), residues: 471 loop : -0.85 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 55 HIS 0.006 0.001 HIS E 182 PHE 0.017 0.001 PHE G 87 TYR 0.024 0.002 TYR F 70 ARG 0.018 0.001 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 5) link_NAG-ASN : angle 3.56646 ( 15) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 1.30497 ( 9) hydrogen bonds : bond 0.03139 ( 306) hydrogen bonds : angle 5.73838 ( 840) SS BOND : bond 0.00306 ( 15) SS BOND : angle 1.15923 ( 30) covalent geometry : bond 0.00307 (12617) covalent geometry : angle 0.66439 (17148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14011.51 seconds wall clock time: 245 minutes 48.01 seconds (14748.01 seconds total)