Starting phenix.real_space_refine on Thu May 15 00:12:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rew_19110/05_2025/8rew_19110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rew_19110/05_2025/8rew_19110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rew_19110/05_2025/8rew_19110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rew_19110/05_2025/8rew_19110.map" model { file = "/net/cci-nas-00/data/ceres_data/8rew_19110/05_2025/8rew_19110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rew_19110/05_2025/8rew_19110.cif" } resolution = 2.98 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= 0.008 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 7869 2.51 5 N 2111 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12428 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1649 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 97} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3795 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 25, 'TRANS': 484} Chain breaks: 3 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "F" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 822 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 911 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: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 946 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 835 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "C" 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: "E" 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 Time building chain proxies: 8.52, per 1000 atoms: 0.69 Number of scatterers: 12428 At special positions: 0 Unit cell: (101.52, 143.28, 149.04, 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 2382 8.00 N 2111 7.00 C 7869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS E 211 " 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 B 326 " - pdb=" SG CYS B 389 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS E 350 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 294 " 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 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 ALPHA1-6 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1000 " - " ASN A 176 " " NAG C 401 " - " ASN C 176 " " NAG C 402 " - " ASN C 82 " " NAG E 701 " - " ASN E 271 " " NAG E 702 " - " ASN E 345 " " NAG J 1 " - " ASN A 136 " " NAG K 1 " - " ASN C 136 " " NAG L 1 " - " ASN E 203 " Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 24 sheets defined 12.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 removed outlier: 3.753A pdb=" N VAL A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.670A pdb=" N LYS A 123 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'B' and resid 281 through 288 removed outlier: 4.015A pdb=" N CYS B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 340 through 346 removed outlier: 3.583A pdb=" N ASN B 344 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN B 345 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 57 removed outlier: 3.640A 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 119 through 124 removed outlier: 4.280A pdb=" N LYS C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 124' 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 211 Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 331 through 337 removed outlier: 3.566A pdb=" N HIS E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.070A pdb=" N HIS E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 104 removed outlier: 3.531A pdb=" N GLU F 104 " --> pdb=" O PRO F 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.576A pdb=" N TYR G 51 " --> pdb=" O PHE G 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.612A pdb=" N ASP H 109 " --> pdb=" O LYS H 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'I' and resid 100 through 104 removed outlier: 3.902A pdb=" N GLU I 104 " --> pdb=" O PRO I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 3.755A pdb=" N LYS A 106 " --> pdb=" O GLN D 378 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL D 376 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N ARG A 110 " --> pdb=" O PRO D 374 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS D 375 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL D 370 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU D 377 " --> pdb=" O TYR D 368 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR D 368 " --> pdb=" O GLU D 377 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU D 379 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE D 366 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN D 381 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 364 " --> pdb=" O ASN D 381 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA D 360 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS D 387 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS D 389 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N CYS D 356 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 313 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR D 369 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.620A 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 134 removed outlier: 5.235A pdb=" N GLY A 216 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN A 172 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR A 181 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AA4, first strand: chain 'B' and resid 299 through 301 Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 313 removed outlier: 7.150A pdb=" N ILE B 311 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TYR B 369 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 386 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 361 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 384 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N MET B 382 " --> pdb=" O PRO B 363 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N SER B 380 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N VAL B 367 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N GLN B 378 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N TYR B 369 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N VAL B 376 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ARG C 110 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL B 376 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 136 removed outlier: 5.270A pdb=" N GLY C 216 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN C 172 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C 181 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 294 through 296 Processing sheet with id=AA8, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.557A pdb=" N ASP E 55 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 78 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 102 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER E 128 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU E 248 " --> pdb=" O ASN E 271 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU E 270 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 320 " --> pdb=" O ASN E 345 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 63 through 64 Processing sheet with id=AB2, first strand: chain 'E' and resid 163 through 164 Processing sheet with id=AB3, first strand: chain 'E' and resid 353 through 356 removed outlier: 3.822A pdb=" N PHE E 354 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 379 " --> pdb=" O PHE E 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 367 through 369 removed outlier: 3.793A pdb=" N LEU E 392 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 541 " --> pdb=" O ARG E 565 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 23 through 25 Processing sheet with id=AB6, first strand: chain 'F' and resid 28 through 31 removed outlier: 4.088A pdb=" N LEU F 29 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 130 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP F 56 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 28 through 31 removed outlier: 4.088A pdb=" N LEU F 29 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 130 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 22 through 26 removed outlier: 5.274A pdb=" N GLY G 35 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 29 through 31 removed outlier: 5.866A pdb=" N GLY G 29 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N MET G 53 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA G 69 " --> pdb=" O MET G 53 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP G 55 " --> pdb=" O VAL G 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 29 through 31 removed outlier: 5.866A pdb=" N GLY G 29 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AC3, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.694A pdb=" N MET H 53 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 23 through 25 Processing sheet with id=AC5, first strand: chain 'I' and resid 30 through 31 removed outlier: 4.636A pdb=" N TYR I 70 " --> pdb=" O PRO I 54 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP I 56 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 30 through 31 382 hydrogen bonds defined for protein. 996 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: 3.68 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2064 1.32 - 1.45: 3394 1.45 - 1.57: 7136 1.57 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 12684 Sorted by residual: bond pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.16e+01 bond pdb=" N SER A 183 " pdb=" CA SER A 183 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.27e-02 6.20e+03 1.15e+01 bond pdb=" N ASN A 184 " pdb=" CA ASN A 184 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" C PRO I 80 " pdb=" O PRO I 80 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.23e-02 6.61e+03 9.50e+00 bond pdb=" CA SER A 183 " pdb=" CB SER A 183 " ideal model delta sigma weight residual 1.534 1.483 0.050 1.76e-02 3.23e+03 8.19e+00 ... (remaining 12679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 16887 2.46 - 4.92: 338 4.92 - 7.38: 35 7.38 - 9.85: 6 9.85 - 12.31: 7 Bond angle restraints: 17273 Sorted by residual: angle pdb=" N PRO A 72 " pdb=" CA PRO A 72 " pdb=" C PRO A 72 " ideal model delta sigma weight residual 111.14 99.45 11.69 1.56e+00 4.11e-01 5.61e+01 angle pdb=" C ILE C 120 " pdb=" N TYR C 121 " pdb=" CA TYR C 121 " ideal model delta sigma weight residual 122.38 110.28 12.10 1.81e+00 3.05e-01 4.47e+01 angle pdb=" N PRO A 69 " pdb=" CA PRO A 69 " pdb=" C PRO A 69 " ideal model delta sigma weight residual 110.70 103.05 7.65 1.22e+00 6.72e-01 3.94e+01 angle pdb=" N SER A 183 " pdb=" CA SER A 183 " pdb=" C SER A 183 " ideal model delta sigma weight residual 109.07 116.95 -7.88 1.52e+00 4.33e-01 2.69e+01 angle pdb=" C ASN I 71 " pdb=" N THR I 72 " pdb=" CA THR I 72 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 ... (remaining 17268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 7317 21.89 - 43.78: 422 43.78 - 65.68: 35 65.68 - 87.57: 20 87.57 - 109.46: 4 Dihedral angle restraints: 7798 sinusoidal: 3166 harmonic: 4632 Sorted by residual: dihedral pdb=" CB CYS B 355 " pdb=" SG CYS B 355 " pdb=" SG CYS D 355 " pdb=" CB CYS D 355 " ideal model delta sinusoidal sigma weight residual 93.00 156.72 -63.72 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS B 293 " pdb=" SG CYS B 293 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual 93.00 149.33 -56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS A 33 " pdb=" SG CYS A 33 " pdb=" SG CYS E 211 " pdb=" CB CYS E 211 " ideal model delta sinusoidal sigma weight residual 93.00 144.07 -51.07 1 1.00e+01 1.00e-02 3.57e+01 ... (remaining 7795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1621 0.054 - 0.108: 311 0.108 - 0.162: 81 0.162 - 0.216: 13 0.216 - 0.270: 7 Chirality restraints: 2033 Sorted by residual: chirality pdb=" CA LEU A 186 " pdb=" N LEU A 186 " pdb=" C LEU A 186 " pdb=" CB LEU A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO A 69 " pdb=" N PRO A 69 " pdb=" C PRO A 69 " pdb=" CB PRO A 69 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2030 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 115 " 0.027 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C GLU C 115 " -0.099 2.00e-02 2.50e+03 pdb=" O GLU C 115 " 0.039 2.00e-02 2.50e+03 pdb=" N THR C 116 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN G 32 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO G 33 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO G 33 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO G 33 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 183 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C SER C 183 " 0.049 2.00e-02 2.50e+03 pdb=" O SER C 183 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN C 184 " -0.016 2.00e-02 2.50e+03 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1725 2.76 - 3.30: 11385 3.30 - 3.83: 21008 3.83 - 4.37: 24954 4.37 - 4.90: 43346 Nonbonded interactions: 102418 Sorted by model distance: nonbonded pdb=" NZ LYS A 56 " pdb=" O SER D 380 " model vdw 2.225 3.120 nonbonded pdb=" OG SER I 84 " pdb=" OG1 THR I 95 " model vdw 2.248 3.040 nonbonded pdb=" O GLY E 386 " pdb=" OG SER E 411 " model vdw 2.264 3.040 nonbonded pdb=" O TYR F 53 " pdb=" NH1 ARG F 121 " model vdw 2.266 3.120 nonbonded pdb=" O LYS C 44 " pdb=" OH TYR D 328 " model vdw 2.291 3.040 ... (remaining 102413 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 267 or resid 1000)) selection = (chain 'C' and (resid 33 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 or (resid 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 through 74 or (resid 75 through 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 77 through 85 or (r \ esid 86 through 87 and (name N or name CA or name C or name O or name CB )) or r \ esid 88 through 164 or (resid 165 and (name N or name CA or name C or name O or \ name CB )) or resid 166 through 225 or (resid 226 and (name N or name CA or name \ C or name O or name CB )) or resid 227 through 267 or resid 402)) } ncs_group { reference = (chain 'B' and ((resid 284 and (name N or name CA or name C or name O or name CB \ )) or resid 285 or (resid 286 and (name N or name CA or name C or name O or nam \ e CB )) or resid 287 through 302 or (resid 303 through 304 and (name N or name C \ A or name C or name O or name CB )) or resid 305 through 361 or (resid 362 and ( \ name N or name CA or name C or name O or name CB )) or resid 363 through 390)) selection = (chain 'D' and (resid 284 through 332 or resid 340 through 390)) } ncs_group { reference = chain 'F' selection = (chain 'I' and resid 21 through 132) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 21 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 131 or (resid 132 a \ nd (name N or name CA or name C or name O or name CB )) or resid 133 through 140 \ )) } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 0.010 Normalize map: mean=0, sd=1: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.500 Find NCS groups from input model: 0.450 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:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.062 12716 Z= 0.235 Angle : 0.833 12.307 17352 Z= 0.441 Chirality : 0.050 0.270 2033 Planarity : 0.006 0.113 2199 Dihedral : 13.545 109.461 4773 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.15 % Allowed : 0.92 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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 (0.20), residues: 1575 helix: -1.38 (0.37), residues: 146 sheet: -0.70 (0.23), residues: 465 loop : -0.72 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 310 HIS 0.013 0.001 HIS E 101 PHE 0.028 0.002 PHE H 48 TYR 0.020 0.002 TYR G 129 ARG 0.015 0.001 ARG A 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 8) link_NAG-ASN : angle 2.34338 ( 24) link_ALPHA1-6 : bond 0.00363 ( 2) link_ALPHA1-6 : angle 1.48173 ( 6) link_BETA1-4 : bond 0.00713 ( 5) link_BETA1-4 : angle 1.37733 ( 15) hydrogen bonds : bond 0.15458 ( 368) hydrogen bonds : angle 7.52105 ( 996) SS BOND : bond 0.00224 ( 17) SS BOND : angle 1.17398 ( 34) covalent geometry : bond 0.00440 (12684) covalent geometry : angle 0.82700 (17273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 265 LEU cc_start: 0.8142 (pt) cc_final: 0.7909 (pt) REVERT: E 101 HIS cc_start: 0.8339 (m-70) cc_final: 0.7922 (m-70) REVERT: E 376 GLU cc_start: 0.7347 (pm20) cc_final: 0.7060 (pm20) REVERT: F 87 ILE cc_start: 0.8375 (mm) cc_final: 0.8162 (mm) REVERT: G 53 MET cc_start: 0.8643 (mmt) cc_final: 0.8179 (mmt) REVERT: I 104 GLU cc_start: 0.8062 (tt0) cc_final: 0.7703 (tt0) REVERT: I 130 THR cc_start: 0.8836 (p) cc_final: 0.8529 (p) outliers start: 2 outliers final: 2 residues processed: 265 average time/residue: 1.1839 time to fit residues: 341.8207 Evaluate side-chains 165 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain G residue 103 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS E 201 HIS ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN G 103 ASN I 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.154802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104074 restraints weight = 20207.288| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.30 r_work: 0.3256 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12716 Z= 0.218 Angle : 0.657 8.732 17352 Z= 0.330 Chirality : 0.044 0.187 2033 Planarity : 0.005 0.077 2199 Dihedral : 8.435 76.821 2046 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.99 % Allowed : 12.56 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1575 helix: -0.75 (0.39), residues: 148 sheet: -0.57 (0.24), residues: 452 loop : -0.53 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 310 HIS 0.008 0.001 HIS E 101 PHE 0.039 0.002 PHE H 48 TYR 0.020 0.002 TYR H 99 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 8) link_NAG-ASN : angle 2.32007 ( 24) link_ALPHA1-6 : bond 0.00459 ( 2) link_ALPHA1-6 : angle 2.02092 ( 6) link_BETA1-4 : bond 0.00434 ( 5) link_BETA1-4 : angle 2.03889 ( 15) hydrogen bonds : bond 0.04062 ( 368) hydrogen bonds : angle 6.11386 ( 996) SS BOND : bond 0.00326 ( 17) SS BOND : angle 1.21717 ( 34) covalent geometry : bond 0.00513 (12684) covalent geometry : angle 0.64652 (17273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6702 (pp20) REVERT: A 128 THR cc_start: 0.9094 (p) cc_final: 0.8675 (t) REVERT: B 297 GLN cc_start: 0.8715 (mt0) cc_final: 0.8497 (mp10) REVERT: C 126 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6478 (mp10) REVERT: C 139 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: C 152 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.7701 (ttp-110) REVERT: C 184 ASN cc_start: 0.7984 (p0) cc_final: 0.7649 (p0) REVERT: D 345 GLN cc_start: 0.8187 (pm20) cc_final: 0.7932 (pm20) REVERT: E 101 HIS cc_start: 0.8610 (m90) cc_final: 0.8117 (m-70) REVERT: E 196 LEU cc_start: 0.7317 (mt) cc_final: 0.7070 (mp) REVERT: E 376 GLU cc_start: 0.7416 (pm20) cc_final: 0.7055 (pm20) REVERT: F 91 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7996 (mtmm) REVERT: F 113 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7578 (pmm) REVERT: G 32 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8649 (mm110) outliers start: 39 outliers final: 16 residues processed: 218 average time/residue: 1.0757 time to fit residues: 258.9652 Evaluate side-chains 189 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.154141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103154 restraints weight = 20427.036| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.35 r_work: 0.3237 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12716 Z= 0.204 Angle : 0.621 7.763 17352 Z= 0.312 Chirality : 0.043 0.208 2033 Planarity : 0.005 0.064 2199 Dihedral : 7.508 65.013 2041 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.13 % Allowed : 15.31 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1575 helix: -0.42 (0.40), residues: 148 sheet: -0.48 (0.24), residues: 430 loop : -0.54 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 310 HIS 0.007 0.001 HIS C 117 PHE 0.031 0.002 PHE H 48 TYR 0.015 0.002 TYR C 171 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 8) link_NAG-ASN : angle 2.36982 ( 24) link_ALPHA1-6 : bond 0.00588 ( 2) link_ALPHA1-6 : angle 1.80202 ( 6) link_BETA1-4 : bond 0.00457 ( 5) link_BETA1-4 : angle 2.03633 ( 15) hydrogen bonds : bond 0.03816 ( 368) hydrogen bonds : angle 5.94763 ( 996) SS BOND : bond 0.00292 ( 17) SS BOND : angle 1.12334 ( 34) covalent geometry : bond 0.00479 (12684) covalent geometry : angle 0.60995 (17273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6670 (pp20) REVERT: A 128 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8711 (t) REVERT: A 142 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: B 292 ASN cc_start: 0.8319 (m110) cc_final: 0.7992 (m-40) REVERT: C 126 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: C 152 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7505 (ttp-110) REVERT: D 359 GLN cc_start: 0.8281 (tp40) cc_final: 0.7999 (tt0) REVERT: E 101 HIS cc_start: 0.8690 (m90) cc_final: 0.8222 (m-70) REVERT: E 125 ARG cc_start: 0.9079 (mtt180) cc_final: 0.8816 (ttp80) REVERT: E 338 LEU cc_start: 0.7919 (tm) cc_final: 0.7557 (tp) REVERT: E 364 CYS cc_start: 0.6752 (t) cc_final: 0.6121 (t) REVERT: E 376 GLU cc_start: 0.7466 (pm20) cc_final: 0.7078 (pm20) REVERT: F 91 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7974 (mtmm) REVERT: F 100 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: G 32 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8591 (mm110) REVERT: H 38 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.8184 (tpp-160) REVERT: H 81 GLU cc_start: 0.8446 (mp0) cc_final: 0.8198 (mp0) outliers start: 54 outliers final: 25 residues processed: 218 average time/residue: 1.0721 time to fit residues: 256.5328 Evaluate side-chains 194 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 106 optimal weight: 3.9990 chunk 110 optimal weight: 0.0170 chunk 122 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 108 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 297 GLN C 117 HIS ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.155026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104479 restraints weight = 20210.580| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.51 r_work: 0.3253 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12716 Z= 0.137 Angle : 0.585 8.551 17352 Z= 0.290 Chirality : 0.042 0.195 2033 Planarity : 0.004 0.058 2199 Dihedral : 6.722 56.818 2041 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.75 % Allowed : 15.70 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1575 helix: -0.29 (0.41), residues: 148 sheet: -0.58 (0.24), residues: 442 loop : -0.48 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 247 HIS 0.006 0.001 HIS C 117 PHE 0.014 0.001 PHE H 48 TYR 0.023 0.001 TYR A 81 ARG 0.008 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 8) link_NAG-ASN : angle 2.25980 ( 24) link_ALPHA1-6 : bond 0.00570 ( 2) link_ALPHA1-6 : angle 1.64307 ( 6) link_BETA1-4 : bond 0.00550 ( 5) link_BETA1-4 : angle 2.27202 ( 15) hydrogen bonds : bond 0.03291 ( 368) hydrogen bonds : angle 5.73907 ( 996) SS BOND : bond 0.00224 ( 17) SS BOND : angle 0.89305 ( 34) covalent geometry : bond 0.00320 (12684) covalent geometry : angle 0.57450 (17273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6694 (pp20) REVERT: A 128 THR cc_start: 0.9083 (p) cc_final: 0.8685 (t) REVERT: A 142 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: B 292 ASN cc_start: 0.8070 (m110) cc_final: 0.7851 (m-40) REVERT: B 313 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8438 (mp0) REVERT: B 362 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8394 (mt-10) REVERT: C 126 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: C 152 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7539 (ttp-110) REVERT: C 233 GLN cc_start: 0.8203 (pm20) cc_final: 0.7131 (pm20) REVERT: D 359 GLN cc_start: 0.8260 (tp40) cc_final: 0.8008 (tt0) REVERT: E 84 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7692 (tt0) REVERT: E 101 HIS cc_start: 0.8617 (m90) cc_final: 0.8099 (m-70) REVERT: E 125 ARG cc_start: 0.8996 (mtt180) cc_final: 0.8789 (ttp80) REVERT: E 152 HIS cc_start: 0.8433 (t-90) cc_final: 0.8189 (t70) REVERT: E 364 CYS cc_start: 0.6620 (t) cc_final: 0.5981 (t) REVERT: E 376 GLU cc_start: 0.7521 (pm20) cc_final: 0.7113 (pm20) REVERT: F 100 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: F 113 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7501 (pmm) REVERT: G 32 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8590 (mm110) REVERT: G 53 MET cc_start: 0.8931 (mmt) cc_final: 0.8700 (mmt) REVERT: H 38 ARG cc_start: 0.8387 (tpt-90) cc_final: 0.8157 (mtp-110) outliers start: 62 outliers final: 23 residues processed: 219 average time/residue: 0.9972 time to fit residues: 241.3265 Evaluate side-chains 194 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.0010 chunk 145 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN E 94 GLN ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103364 restraints weight = 20229.265| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.32 r_work: 0.3243 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12716 Z= 0.159 Angle : 0.597 8.734 17352 Z= 0.296 Chirality : 0.042 0.209 2033 Planarity : 0.004 0.053 2199 Dihedral : 6.165 51.057 2041 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.13 % Allowed : 17.38 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1575 helix: -0.26 (0.40), residues: 152 sheet: -0.59 (0.24), residues: 442 loop : -0.50 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.004 0.001 HIS D 346 PHE 0.018 0.001 PHE H 48 TYR 0.026 0.001 TYR A 81 ARG 0.006 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 8) link_NAG-ASN : angle 2.28237 ( 24) link_ALPHA1-6 : bond 0.00624 ( 2) link_ALPHA1-6 : angle 1.67336 ( 6) link_BETA1-4 : bond 0.00542 ( 5) link_BETA1-4 : angle 2.45373 ( 15) hydrogen bonds : bond 0.03374 ( 368) hydrogen bonds : angle 5.63679 ( 996) SS BOND : bond 0.00300 ( 17) SS BOND : angle 0.97406 ( 34) covalent geometry : bond 0.00374 (12684) covalent geometry : angle 0.58575 (17273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: A 128 THR cc_start: 0.9103 (p) cc_final: 0.8720 (t) REVERT: A 142 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: B 313 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: B 362 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8413 (mt-10) REVERT: C 126 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: C 152 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7505 (ttp-110) REVERT: C 177 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8491 (m-40) REVERT: C 233 GLN cc_start: 0.8247 (pm20) cc_final: 0.7931 (pm20) REVERT: D 359 GLN cc_start: 0.8232 (tp40) cc_final: 0.7974 (tt0) REVERT: E 84 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7762 (tt0) REVERT: E 101 HIS cc_start: 0.8683 (m90) cc_final: 0.8189 (m-70) REVERT: E 125 ARG cc_start: 0.9080 (mtt180) cc_final: 0.8776 (ttp80) REVERT: E 152 HIS cc_start: 0.8341 (t-90) cc_final: 0.8126 (t70) REVERT: E 338 LEU cc_start: 0.7577 (tm) cc_final: 0.7248 (tp) REVERT: E 364 CYS cc_start: 0.6566 (t) cc_final: 0.5954 (t) REVERT: E 376 GLU cc_start: 0.7539 (pm20) cc_final: 0.7145 (pm20) REVERT: F 91 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8029 (mtmm) REVERT: F 100 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: G 32 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8584 (mm110) REVERT: G 53 MET cc_start: 0.9016 (mmt) cc_final: 0.8515 (mmt) REVERT: G 124 THR cc_start: 0.9490 (m) cc_final: 0.9221 (p) REVERT: H 47 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8061 (p) REVERT: I 104 GLU cc_start: 0.8433 (tt0) cc_final: 0.7796 (pp20) outliers start: 54 outliers final: 31 residues processed: 210 average time/residue: 0.9749 time to fit residues: 226.9563 Evaluate side-chains 202 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.0050 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 118 ASN B 297 GLN C 177 ASN ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103253 restraints weight = 20436.610| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.54 r_work: 0.3238 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12716 Z= 0.155 Angle : 0.592 8.267 17352 Z= 0.292 Chirality : 0.042 0.208 2033 Planarity : 0.004 0.065 2199 Dihedral : 5.819 49.564 2041 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.44 % Allowed : 17.84 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1575 helix: -0.18 (0.40), residues: 152 sheet: -0.59 (0.24), residues: 440 loop : -0.51 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS E 181 PHE 0.014 0.001 PHE H 48 TYR 0.021 0.001 TYR A 81 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 8) link_NAG-ASN : angle 2.24091 ( 24) link_ALPHA1-6 : bond 0.00663 ( 2) link_ALPHA1-6 : angle 1.65351 ( 6) link_BETA1-4 : bond 0.00584 ( 5) link_BETA1-4 : angle 2.50686 ( 15) hydrogen bonds : bond 0.03278 ( 368) hydrogen bonds : angle 5.55108 ( 996) SS BOND : bond 0.00259 ( 17) SS BOND : angle 0.94699 ( 34) covalent geometry : bond 0.00365 (12684) covalent geometry : angle 0.58009 (17273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 173 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8709 (m-40) cc_final: 0.8415 (m110) REVERT: A 128 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 142 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: B 292 ASN cc_start: 0.8249 (m110) cc_final: 0.7757 (m-40) REVERT: B 303 ARG cc_start: 0.7493 (tpm170) cc_final: 0.7268 (tpm170) REVERT: B 309 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8375 (mmtm) REVERT: B 313 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: B 362 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8401 (mt-10) REVERT: B 378 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: C 126 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: C 152 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7485 (ttp-110) REVERT: C 233 GLN cc_start: 0.8243 (pm20) cc_final: 0.7940 (pm20) REVERT: D 345 GLN cc_start: 0.8275 (pm20) cc_final: 0.7847 (pm20) REVERT: D 359 GLN cc_start: 0.8234 (tp40) cc_final: 0.7986 (tt0) REVERT: E 84 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7753 (tt0) REVERT: E 101 HIS cc_start: 0.8678 (m90) cc_final: 0.8163 (m-70) REVERT: E 125 ARG cc_start: 0.9036 (mtt180) cc_final: 0.8759 (ttp80) REVERT: E 152 HIS cc_start: 0.8382 (t-90) cc_final: 0.8148 (t70) REVERT: E 348 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4576 (mtm180) REVERT: E 364 CYS cc_start: 0.6661 (t) cc_final: 0.6035 (t) REVERT: E 376 GLU cc_start: 0.7524 (pm20) cc_final: 0.7122 (pm20) REVERT: F 100 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: G 32 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8626 (mm110) REVERT: G 124 THR cc_start: 0.9473 (m) cc_final: 0.9240 (p) REVERT: H 38 ARG cc_start: 0.8466 (mtp-110) cc_final: 0.8252 (mmm-85) REVERT: H 47 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8110 (p) REVERT: I 104 GLU cc_start: 0.8459 (tt0) cc_final: 0.7820 (pp20) outliers start: 58 outliers final: 33 residues processed: 212 average time/residue: 0.9826 time to fit residues: 230.4833 Evaluate side-chains 207 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 117 HIS ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103605 restraints weight = 20351.576| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.43 r_work: 0.3249 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12716 Z= 0.143 Angle : 0.593 9.950 17352 Z= 0.292 Chirality : 0.042 0.206 2033 Planarity : 0.004 0.052 2199 Dihedral : 5.510 47.674 2041 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.67 % Allowed : 18.07 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1575 helix: -0.21 (0.40), residues: 153 sheet: -0.59 (0.24), residues: 437 loop : -0.46 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.010 0.001 HIS A 117 PHE 0.011 0.001 PHE C 217 TYR 0.018 0.001 TYR A 81 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 8) link_NAG-ASN : angle 2.24391 ( 24) link_ALPHA1-6 : bond 0.00626 ( 2) link_ALPHA1-6 : angle 1.58127 ( 6) link_BETA1-4 : bond 0.00616 ( 5) link_BETA1-4 : angle 2.54499 ( 15) hydrogen bonds : bond 0.03209 ( 368) hydrogen bonds : angle 5.50817 ( 996) SS BOND : bond 0.00264 ( 17) SS BOND : angle 1.14858 ( 34) covalent geometry : bond 0.00337 (12684) covalent geometry : angle 0.58058 (17273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 142 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7477 (mt-10) REVERT: B 303 ARG cc_start: 0.7539 (tpm170) cc_final: 0.7330 (tpm170) REVERT: B 313 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: B 362 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 378 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7724 (tp40) REVERT: C 126 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6533 (mp10) REVERT: C 139 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8245 (mm-30) REVERT: C 152 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7478 (ttp-110) REVERT: C 233 GLN cc_start: 0.8262 (pm20) cc_final: 0.7949 (pm20) REVERT: D 359 GLN cc_start: 0.8208 (tp40) cc_final: 0.7975 (tt0) REVERT: E 84 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7745 (tt0) REVERT: E 101 HIS cc_start: 0.8695 (m90) cc_final: 0.8186 (m-70) REVERT: E 125 ARG cc_start: 0.9050 (mtt180) cc_final: 0.8757 (ttp80) REVERT: E 152 HIS cc_start: 0.8368 (t-90) cc_final: 0.8161 (t70) REVERT: E 338 LEU cc_start: 0.7271 (tm) cc_final: 0.6939 (tp) REVERT: E 348 ARG cc_start: 0.5090 (OUTLIER) cc_final: 0.4499 (mtm180) REVERT: E 364 CYS cc_start: 0.6675 (t) cc_final: 0.6075 (t) REVERT: E 376 GLU cc_start: 0.7513 (pm20) cc_final: 0.7067 (pm20) REVERT: F 100 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: G 32 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8649 (mm110) REVERT: H 38 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.8230 (mmm-85) REVERT: H 47 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8084 (p) REVERT: I 104 GLU cc_start: 0.8464 (tt0) cc_final: 0.7832 (pp20) outliers start: 61 outliers final: 34 residues processed: 210 average time/residue: 1.0151 time to fit residues: 237.3830 Evaluate side-chains 206 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 117 HIS ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.154469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103537 restraints weight = 20431.865| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.34 r_work: 0.3251 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12716 Z= 0.144 Angle : 0.604 10.383 17352 Z= 0.297 Chirality : 0.042 0.205 2033 Planarity : 0.004 0.052 2199 Dihedral : 5.242 44.739 2041 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.13 % Allowed : 18.68 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.20), residues: 1575 helix: -0.17 (0.41), residues: 153 sheet: -0.59 (0.24), residues: 438 loop : -0.45 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.011 0.001 HIS A 117 PHE 0.011 0.001 PHE C 217 TYR 0.018 0.001 TYR A 81 ARG 0.005 0.000 ARG F 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 2.22178 ( 24) link_ALPHA1-6 : bond 0.00617 ( 2) link_ALPHA1-6 : angle 1.57697 ( 6) link_BETA1-4 : bond 0.00641 ( 5) link_BETA1-4 : angle 2.53911 ( 15) hydrogen bonds : bond 0.03213 ( 368) hydrogen bonds : angle 5.49323 ( 996) SS BOND : bond 0.00243 ( 17) SS BOND : angle 1.20720 ( 34) covalent geometry : bond 0.00340 (12684) covalent geometry : angle 0.59167 (17273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8690 (t) REVERT: A 142 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 313 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: B 362 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 378 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7711 (tp40) REVERT: C 126 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6497 (mp10) REVERT: C 139 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: C 152 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7519 (ttp-110) REVERT: C 233 GLN cc_start: 0.8258 (pm20) cc_final: 0.7954 (pm20) REVERT: D 345 GLN cc_start: 0.8294 (pm20) cc_final: 0.7836 (pm20) REVERT: D 359 GLN cc_start: 0.8208 (tp40) cc_final: 0.7979 (tt0) REVERT: E 84 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7792 (tt0) REVERT: E 101 HIS cc_start: 0.8759 (m90) cc_final: 0.8274 (m-70) REVERT: E 125 ARG cc_start: 0.9169 (mtt180) cc_final: 0.8799 (ttp80) REVERT: E 152 HIS cc_start: 0.8313 (t-90) cc_final: 0.8111 (t70) REVERT: E 338 LEU cc_start: 0.7238 (tm) cc_final: 0.6904 (tp) REVERT: E 348 ARG cc_start: 0.5081 (OUTLIER) cc_final: 0.4491 (mtm180) REVERT: E 364 CYS cc_start: 0.6550 (t) cc_final: 0.5932 (t) REVERT: E 376 GLU cc_start: 0.7507 (pm20) cc_final: 0.7127 (pm20) REVERT: F 100 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: G 22 GLN cc_start: 0.8256 (pp30) cc_final: 0.7776 (pm20) REVERT: G 32 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8573 (tp40) REVERT: G 53 MET cc_start: 0.8993 (mmt) cc_final: 0.8636 (mmt) REVERT: H 47 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8055 (p) REVERT: I 104 GLU cc_start: 0.8447 (tt0) cc_final: 0.7818 (pp20) outliers start: 54 outliers final: 34 residues processed: 207 average time/residue: 1.0141 time to fit residues: 232.3223 Evaluate side-chains 208 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 117 HIS ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.154104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104012 restraints weight = 20574.303| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.38 r_work: 0.3255 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12716 Z= 0.164 Angle : 0.610 10.580 17352 Z= 0.300 Chirality : 0.042 0.216 2033 Planarity : 0.004 0.052 2199 Dihedral : 5.083 41.239 2041 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.29 % Allowed : 19.07 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1575 helix: -0.08 (0.41), residues: 152 sheet: -0.65 (0.24), residues: 445 loop : -0.46 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 66 HIS 0.012 0.001 HIS A 117 PHE 0.012 0.001 PHE G 48 TYR 0.020 0.001 TYR A 81 ARG 0.005 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 8) link_NAG-ASN : angle 2.27015 ( 24) link_ALPHA1-6 : bond 0.00602 ( 2) link_ALPHA1-6 : angle 1.57106 ( 6) link_BETA1-4 : bond 0.00653 ( 5) link_BETA1-4 : angle 2.49650 ( 15) hydrogen bonds : bond 0.03296 ( 368) hydrogen bonds : angle 5.47842 ( 996) SS BOND : bond 0.00262 ( 17) SS BOND : angle 1.17159 ( 34) covalent geometry : bond 0.00388 (12684) covalent geometry : angle 0.59791 (17273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8648 (t) REVERT: A 142 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 313 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: B 362 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 378 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7748 (tp40) REVERT: C 126 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6532 (mp10) REVERT: C 139 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8371 (mm-30) REVERT: C 152 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7585 (ttp-110) REVERT: C 233 GLN cc_start: 0.8250 (pm20) cc_final: 0.7963 (pm20) REVERT: D 345 GLN cc_start: 0.8378 (pm20) cc_final: 0.7973 (pm20) REVERT: D 359 GLN cc_start: 0.8216 (tp40) cc_final: 0.7985 (tt0) REVERT: E 84 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7745 (tt0) REVERT: E 101 HIS cc_start: 0.8589 (m90) cc_final: 0.8065 (m-70) REVERT: E 152 HIS cc_start: 0.8355 (t-90) cc_final: 0.8150 (t70) REVERT: E 348 ARG cc_start: 0.5526 (OUTLIER) cc_final: 0.4865 (mtm180) REVERT: E 364 CYS cc_start: 0.6909 (t) cc_final: 0.6237 (t) REVERT: E 376 GLU cc_start: 0.7489 (pm20) cc_final: 0.6987 (pm20) REVERT: F 100 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: G 22 GLN cc_start: 0.8309 (pp30) cc_final: 0.7848 (pm20) REVERT: G 32 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8594 (tp40) REVERT: H 47 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8155 (p) REVERT: I 104 GLU cc_start: 0.8439 (tt0) cc_final: 0.7837 (pp20) outliers start: 56 outliers final: 34 residues processed: 206 average time/residue: 1.0174 time to fit residues: 231.8054 Evaluate side-chains 207 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 163 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 364 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 31 optimal weight: 0.6980 chunk 108 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 117 HIS ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.154504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104748 restraints weight = 20412.320| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.33 r_work: 0.3267 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12716 Z= 0.153 Angle : 0.622 10.335 17352 Z= 0.305 Chirality : 0.043 0.261 2033 Planarity : 0.004 0.070 2199 Dihedral : 4.963 41.014 2041 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.37 % Allowed : 20.37 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1575 helix: -0.22 (0.40), residues: 160 sheet: -0.65 (0.24), residues: 441 loop : -0.44 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.012 0.001 HIS A 117 PHE 0.011 0.001 PHE C 217 TYR 0.020 0.001 TYR A 81 ARG 0.020 0.001 ARG E 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 8) link_NAG-ASN : angle 2.25313 ( 24) link_ALPHA1-6 : bond 0.00608 ( 2) link_ALPHA1-6 : angle 1.56223 ( 6) link_BETA1-4 : bond 0.00654 ( 5) link_BETA1-4 : angle 2.37362 ( 15) hydrogen bonds : bond 0.03243 ( 368) hydrogen bonds : angle 5.45301 ( 996) SS BOND : bond 0.00259 ( 17) SS BOND : angle 1.09669 ( 34) covalent geometry : bond 0.00364 (12684) covalent geometry : angle 0.61070 (17273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 166 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9028 (p) cc_final: 0.8641 (t) REVERT: A 142 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 313 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8449 (mp0) REVERT: B 362 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 126 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6506 (mp10) REVERT: C 139 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: C 152 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7579 (ttp-110) REVERT: C 233 GLN cc_start: 0.8235 (pm20) cc_final: 0.7951 (pm20) REVERT: D 345 GLN cc_start: 0.8376 (pm20) cc_final: 0.7967 (pm20) REVERT: D 359 GLN cc_start: 0.8235 (tp40) cc_final: 0.7998 (tt0) REVERT: D 375 LYS cc_start: 0.7935 (mttt) cc_final: 0.7700 (mtpt) REVERT: E 84 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7721 (tt0) REVERT: E 101 HIS cc_start: 0.8597 (m90) cc_final: 0.8071 (m-70) REVERT: E 338 LEU cc_start: 0.7277 (tm) cc_final: 0.6925 (tp) REVERT: E 348 ARG cc_start: 0.5477 (OUTLIER) cc_final: 0.4819 (mtm180) REVERT: E 364 CYS cc_start: 0.6862 (t) cc_final: 0.6193 (t) REVERT: E 376 GLU cc_start: 0.7475 (pm20) cc_final: 0.6977 (pm20) REVERT: F 100 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: G 22 GLN cc_start: 0.8314 (pp30) cc_final: 0.7843 (pm20) REVERT: G 32 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8556 (tp40) REVERT: G 53 MET cc_start: 0.8962 (mmt) cc_final: 0.8639 (mmt) REVERT: H 47 THR cc_start: 0.8506 (p) cc_final: 0.8149 (p) REVERT: I 104 GLU cc_start: 0.8434 (tt0) cc_final: 0.7831 (pp20) outliers start: 44 outliers final: 32 residues processed: 193 average time/residue: 1.0400 time to fit residues: 221.2792 Evaluate side-chains 201 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 90 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 0.0270 chunk 38 optimal weight: 0.0020 chunk 80 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 150 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.156863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.107496 restraints weight = 20527.098| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.33 r_work: 0.3325 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12716 Z= 0.108 Angle : 0.604 12.262 17352 Z= 0.294 Chirality : 0.042 0.232 2033 Planarity : 0.004 0.049 2199 Dihedral : 4.656 36.939 2041 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.99 % Allowed : 21.13 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1575 helix: -0.05 (0.41), residues: 152 sheet: -0.51 (0.24), residues: 450 loop : -0.41 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 72 HIS 0.011 0.001 HIS A 117 PHE 0.010 0.001 PHE C 217 TYR 0.017 0.001 TYR A 81 ARG 0.016 0.000 ARG E 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 8) link_NAG-ASN : angle 2.09332 ( 24) link_ALPHA1-6 : bond 0.00601 ( 2) link_ALPHA1-6 : angle 1.47057 ( 6) link_BETA1-4 : bond 0.00731 ( 5) link_BETA1-4 : angle 2.22475 ( 15) hydrogen bonds : bond 0.02950 ( 368) hydrogen bonds : angle 5.31438 ( 996) SS BOND : bond 0.00213 ( 17) SS BOND : angle 0.91552 ( 34) covalent geometry : bond 0.00257 (12684) covalent geometry : angle 0.59423 (17273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9958.61 seconds wall clock time: 172 minutes 35.32 seconds (10355.32 seconds total)