Starting phenix.real_space_refine on Wed Jul 30 14:09:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rew_19110/07_2025/8rew_19110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rew_19110/07_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_19110/07_2025/8rew_19110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rew_19110/07_2025/8rew_19110.map" model { file = "/net/cci-nas-00/data/ceres_data/8rew_19110/07_2025/8rew_19110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rew_19110/07_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-5711/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: 8.63, 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 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: 1.63 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: 3.79 Time building geometry restraints manager: 3.62 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: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.400 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- 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 : 1.367 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: 1.1576 time to fit residues: 334.2678 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 : 1.283 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103892 restraints weight = 20207.323| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.32 r_work: 0.3254 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 2.02088 ( 6) link_BETA1-4 : bond 0.00434 ( 5) link_BETA1-4 : angle 2.03893 ( 15) hydrogen bonds : bond 0.04062 ( 368) hydrogen bonds : angle 6.11387 ( 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 : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6674 (pp20) REVERT: A 128 THR cc_start: 0.9105 (p) cc_final: 0.8682 (t) REVERT: B 297 GLN cc_start: 0.8714 (mt0) cc_final: 0.8494 (mp10) REVERT: C 126 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6474 (mp10) REVERT: C 139 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: C 152 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7682 (ttp-110) REVERT: C 184 ASN cc_start: 0.7990 (p0) cc_final: 0.7654 (p0) REVERT: D 345 GLN cc_start: 0.8172 (pm20) cc_final: 0.7910 (pm20) REVERT: E 101 HIS cc_start: 0.8671 (m90) cc_final: 0.8186 (m-70) REVERT: E 196 LEU cc_start: 0.7293 (mt) cc_final: 0.7049 (mp) REVERT: E 338 LEU cc_start: 0.8231 (tm) cc_final: 0.8019 (tm) REVERT: E 376 GLU cc_start: 0.7418 (pm20) cc_final: 0.7088 (pm20) REVERT: F 91 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7964 (mtmm) REVERT: F 113 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7581 (pmm) REVERT: G 32 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8644 (mm110) outliers start: 39 outliers final: 16 residues processed: 218 average time/residue: 1.2334 time to fit residues: 295.7741 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 : 1.571 ------------------------------------------------------------------------------- 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: 0.5980 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.155793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105264 restraints weight = 20377.468| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.36 r_work: 0.3272 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12716 Z= 0.152 Angle : 0.593 7.833 17352 Z= 0.298 Chirality : 0.042 0.199 2033 Planarity : 0.004 0.064 2199 Dihedral : 7.408 65.171 2041 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.91 % Allowed : 15.39 % Favored : 80.70 % 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: -0.83 (0.20), residues: 1575 helix: -0.40 (0.40), residues: 148 sheet: -0.57 (0.24), residues: 447 loop : -0.50 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 247 HIS 0.007 0.001 HIS C 117 PHE 0.022 0.001 PHE H 48 TYR 0.016 0.001 TYR C 171 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 8) link_NAG-ASN : angle 2.25549 ( 24) link_ALPHA1-6 : bond 0.00526 ( 2) link_ALPHA1-6 : angle 1.71707 ( 6) link_BETA1-4 : bond 0.00488 ( 5) link_BETA1-4 : angle 2.04740 ( 15) hydrogen bonds : bond 0.03566 ( 368) hydrogen bonds : angle 5.87935 ( 996) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.95858 ( 34) covalent geometry : bond 0.00356 (12684) covalent geometry : angle 0.58241 (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 242 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6725 (pp20) REVERT: A 128 THR cc_start: 0.9089 (p) cc_final: 0.8707 (t) REVERT: A 142 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: B 292 ASN cc_start: 0.8308 (m110) cc_final: 0.7936 (m-40) REVERT: B 297 GLN cc_start: 0.8712 (mt0) cc_final: 0.8508 (mp10) REVERT: B 309 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8382 (mmtm) REVERT: C 119 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: C 126 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6511 (mp10) REVERT: C 152 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.7577 (ttp-110) REVERT: C 184 ASN cc_start: 0.8126 (p0) cc_final: 0.7724 (p0) REVERT: D 359 GLN cc_start: 0.8290 (tp40) cc_final: 0.8030 (tt0) REVERT: E 101 HIS cc_start: 0.8666 (m90) cc_final: 0.8191 (m-70) REVERT: E 125 ARG cc_start: 0.9041 (mtt180) cc_final: 0.8810 (ttp80) REVERT: E 152 HIS cc_start: 0.8449 (t-90) cc_final: 0.8164 (t70) REVERT: E 338 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7900 (tp) REVERT: E 364 CYS cc_start: 0.6690 (t) cc_final: 0.6034 (t) REVERT: E 376 GLU cc_start: 0.7466 (pm20) cc_final: 0.7091 (pm20) REVERT: F 91 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7988 (mtmm) REVERT: F 100 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: G 32 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8554 (mm110) REVERT: H 38 ARG cc_start: 0.8389 (tpt-90) cc_final: 0.8124 (tpp-160) outliers start: 51 outliers final: 21 residues processed: 222 average time/residue: 1.1486 time to fit residues: 279.5221 Evaluate side-chains 193 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 C residue 109 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 126 GLN 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 338 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 106 optimal weight: 0.0980 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101725 restraints weight = 20257.607| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.46 r_work: 0.3214 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12716 Z= 0.219 Angle : 0.625 8.447 17352 Z= 0.311 Chirality : 0.043 0.214 2033 Planarity : 0.005 0.058 2199 Dihedral : 6.890 57.373 2041 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.13 % Allowed : 15.31 % 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: -0.91 (0.20), residues: 1575 helix: -0.45 (0.39), residues: 154 sheet: -0.62 (0.24), residues: 446 loop : -0.56 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 66 HIS 0.006 0.001 HIS C 117 PHE 0.029 0.002 PHE H 48 TYR 0.025 0.002 TYR A 81 ARG 0.010 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 8) link_NAG-ASN : angle 2.39496 ( 24) link_ALPHA1-6 : bond 0.00602 ( 2) link_ALPHA1-6 : angle 1.77332 ( 6) link_BETA1-4 : bond 0.00465 ( 5) link_BETA1-4 : angle 2.22821 ( 15) hydrogen bonds : bond 0.03706 ( 368) hydrogen bonds : angle 5.79953 ( 996) SS BOND : bond 0.00306 ( 17) SS BOND : angle 1.10933 ( 34) covalent geometry : bond 0.00514 (12684) covalent geometry : angle 0.61385 (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 244 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6685 (pp20) REVERT: A 128 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8722 (t) REVERT: A 142 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: B 313 GLU cc_start: 0.8740 (mp0) cc_final: 0.8528 (mp0) REVERT: B 362 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8409 (mt-10) REVERT: B 378 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7820 (tp40) REVERT: C 119 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: C 126 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6466 (mp10) REVERT: C 152 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7510 (ttp-110) REVERT: C 233 GLN cc_start: 0.8265 (pm20) cc_final: 0.7236 (pm20) REVERT: D 359 GLN cc_start: 0.8276 (tp40) cc_final: 0.7989 (tt0) REVERT: E 84 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7739 (tt0) REVERT: E 101 HIS cc_start: 0.8692 (m90) cc_final: 0.8199 (m-70) REVERT: E 125 ARG cc_start: 0.9139 (mtt180) cc_final: 0.8840 (ttp80) REVERT: E 152 HIS cc_start: 0.8428 (t-90) cc_final: 0.8149 (t70) REVERT: E 338 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7853 (tp) REVERT: E 364 CYS cc_start: 0.6560 (t) cc_final: 0.5908 (t) REVERT: E 376 GLU cc_start: 0.7535 (pm20) cc_final: 0.7153 (pm20) REVERT: F 100 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: G 32 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8580 (mm110) REVERT: G 53 MET cc_start: 0.9029 (mmt) cc_final: 0.8685 (mmt) REVERT: G 127 MET cc_start: 0.9161 (mtm) cc_final: 0.8619 (mtm) REVERT: H 38 ARG cc_start: 0.8453 (tpt-90) cc_final: 0.8203 (mtp-110) REVERT: H 47 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8011 (p) REVERT: I 66 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8158 (mtm110) outliers start: 67 outliers final: 31 residues processed: 223 average time/residue: 1.0065 time to fit residues: 248.2696 Evaluate side-chains 212 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 B residue 378 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 GLU 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 231 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 338 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 G residue 24 VAL Chi-restraints excluded: chain G residue 37 LEU 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 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 97 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 Chi-restraints excluded: chain I residue 66 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.154430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103356 restraints weight = 20212.433| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.47 r_work: 0.3251 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2241 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= 0.147 Angle : 0.592 8.716 17352 Z= 0.294 Chirality : 0.042 0.201 2033 Planarity : 0.004 0.054 2199 Dihedral : 6.252 50.998 2041 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.29 % Allowed : 17.76 % Favored : 77.95 % 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: -0.86 (0.20), residues: 1575 helix: -0.24 (0.40), residues: 152 sheet: -0.62 (0.23), residues: 449 loop : -0.54 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 247 HIS 0.003 0.001 HIS E 181 PHE 0.014 0.001 PHE H 48 TYR 0.025 0.001 TYR A 81 ARG 0.005 0.000 ARG C 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 8) link_NAG-ASN : angle 2.27949 ( 24) link_ALPHA1-6 : bond 0.00612 ( 2) link_ALPHA1-6 : angle 1.64172 ( 6) link_BETA1-4 : bond 0.00546 ( 5) link_BETA1-4 : angle 2.40699 ( 15) hydrogen bonds : bond 0.03289 ( 368) hydrogen bonds : angle 5.66341 ( 996) SS BOND : bond 0.00275 ( 17) SS BOND : angle 0.88365 ( 34) covalent geometry : bond 0.00344 (12684) covalent geometry : angle 0.58053 (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 238 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6682 (pp20) REVERT: A 118 ASN cc_start: 0.8667 (m-40) cc_final: 0.8284 (m110) REVERT: A 128 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 142 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: B 313 GLU cc_start: 0.8718 (mp0) cc_final: 0.8395 (mp0) REVERT: B 362 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8357 (mt-10) REVERT: B 378 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7757 (tp40) REVERT: C 126 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: C 152 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7526 (ttp-110) REVERT: C 233 GLN cc_start: 0.8229 (pm20) cc_final: 0.7922 (pm20) REVERT: D 345 GLN cc_start: 0.8311 (pm20) cc_final: 0.7828 (pm20) REVERT: D 359 GLN cc_start: 0.8257 (tp40) cc_final: 0.8007 (tt0) REVERT: E 84 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7766 (tt0) REVERT: E 101 HIS cc_start: 0.8715 (m90) cc_final: 0.8229 (m-70) REVERT: E 125 ARG cc_start: 0.9099 (mtt180) cc_final: 0.8783 (ttp80) REVERT: E 152 HIS cc_start: 0.8307 (t-90) cc_final: 0.8083 (t70) REVERT: E 364 CYS cc_start: 0.6427 (t) cc_final: 0.5824 (t) REVERT: E 376 GLU cc_start: 0.7510 (pm20) cc_final: 0.7129 (pm20) REVERT: F 91 LYS cc_start: 0.8300 (mtpp) cc_final: 0.8041 (mtmm) REVERT: F 100 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: G 32 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8560 (mm110) REVERT: G 53 MET cc_start: 0.8987 (mmt) cc_final: 0.8649 (mmt) REVERT: G 124 THR cc_start: 0.9462 (m) cc_final: 0.9220 (p) REVERT: H 47 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8070 (p) REVERT: I 66 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8074 (mtm110) REVERT: I 104 GLU cc_start: 0.8429 (tt0) cc_final: 0.7795 (pp20) outliers start: 56 outliers final: 29 residues processed: 218 average time/residue: 1.1099 time to fit residues: 265.7952 Evaluate side-chains 207 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 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 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 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 77 SER 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 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 66 ARG 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: 10.0000 chunk 6 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.154225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103607 restraints weight = 20477.106| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.51 r_work: 0.3238 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12716 Z= 0.153 Angle : 0.588 8.452 17352 Z= 0.291 Chirality : 0.042 0.208 2033 Planarity : 0.004 0.058 2199 Dihedral : 5.752 49.594 2041 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.98 % Allowed : 17.46 % Favored : 77.57 % 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: -0.86 (0.20), residues: 1575 helix: -0.24 (0.40), residues: 153 sheet: -0.60 (0.23), residues: 451 loop : -0.55 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.008 0.001 HIS A 117 PHE 0.012 0.001 PHE G 48 TYR 0.022 0.001 TYR A 81 ARG 0.011 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 2.29588 ( 24) link_ALPHA1-6 : bond 0.00599 ( 2) link_ALPHA1-6 : angle 1.63710 ( 6) link_BETA1-4 : bond 0.00564 ( 5) link_BETA1-4 : angle 2.49031 ( 15) hydrogen bonds : bond 0.03302 ( 368) hydrogen bonds : angle 5.53954 ( 996) SS BOND : bond 0.00264 ( 17) SS BOND : angle 0.95250 ( 34) covalent geometry : bond 0.00361 (12684) covalent geometry : angle 0.57649 (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 238 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6714 (pp20) REVERT: A 128 THR cc_start: 0.9093 (p) cc_final: 0.8698 (t) REVERT: A 142 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 305 ASP cc_start: 0.8396 (t0) cc_final: 0.8196 (t0) REVERT: B 313 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: B 362 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 378 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7752 (tp40) REVERT: C 126 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: C 139 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: C 152 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7445 (ttp-110) REVERT: C 233 GLN cc_start: 0.8270 (pm20) cc_final: 0.7965 (pm20) REVERT: D 345 GLN cc_start: 0.8282 (pm20) cc_final: 0.7888 (pm20) REVERT: D 359 GLN cc_start: 0.8243 (tp40) cc_final: 0.7993 (tt0) REVERT: E 84 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7708 (tt0) REVERT: E 101 HIS cc_start: 0.8628 (m90) cc_final: 0.8118 (m-70) REVERT: E 125 ARG cc_start: 0.9065 (mtt180) cc_final: 0.8781 (ttp80) REVERT: E 152 HIS cc_start: 0.8365 (t-90) cc_final: 0.8144 (t70) REVERT: E 348 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.4742 (mtm180) REVERT: E 364 CYS cc_start: 0.6704 (t) cc_final: 0.6047 (t) REVERT: E 376 GLU cc_start: 0.7531 (pm20) cc_final: 0.7110 (pm20) REVERT: F 100 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: G 32 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8556 (mm110) REVERT: G 122 ASP cc_start: 0.8229 (p0) cc_final: 0.7977 (p0) REVERT: G 124 THR cc_start: 0.9473 (m) cc_final: 0.9245 (p) REVERT: H 47 THR cc_start: 0.8383 (p) cc_final: 0.8043 (p) REVERT: I 66 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8052 (mtm110) REVERT: I 104 GLU cc_start: 0.8433 (tt0) cc_final: 0.7804 (pp20) outliers start: 65 outliers final: 31 residues processed: 216 average time/residue: 1.0653 time to fit residues: 253.6331 Evaluate side-chains 210 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 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 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 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 Chi-restraints excluded: chain I residue 66 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** I 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103608 restraints weight = 20277.009| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.29 r_work: 0.3250 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2486 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= 0.150 Angle : 0.604 9.761 17352 Z= 0.297 Chirality : 0.042 0.208 2033 Planarity : 0.004 0.053 2199 Dihedral : 5.481 47.525 2041 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.44 % Allowed : 18.68 % Favored : 76.88 % 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: -0.83 (0.20), residues: 1575 helix: -0.25 (0.40), residues: 153 sheet: -0.60 (0.23), residues: 448 loop : -0.51 (0.19), residues: 974 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 0.019 0.001 TYR A 81 ARG 0.006 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 2.26869 ( 24) link_ALPHA1-6 : bond 0.00570 ( 2) link_ALPHA1-6 : angle 1.58515 ( 6) link_BETA1-4 : bond 0.00624 ( 5) link_BETA1-4 : angle 2.55013 ( 15) hydrogen bonds : bond 0.03236 ( 368) hydrogen bonds : angle 5.48549 ( 996) SS BOND : bond 0.00306 ( 17) SS BOND : angle 1.04010 ( 34) covalent geometry : bond 0.00351 (12684) covalent geometry : angle 0.59231 (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 237 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: A 128 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 142 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: B 303 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8244 (mmm160) REVERT: B 305 ASP cc_start: 0.8385 (t0) cc_final: 0.8169 (t0) REVERT: B 313 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: B 362 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8361 (mt-10) REVERT: B 378 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7726 (tp40) REVERT: C 126 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6455 (mp10) REVERT: C 139 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8253 (mm-30) REVERT: C 152 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.7487 (ttp-110) REVERT: C 233 GLN cc_start: 0.8278 (pm20) cc_final: 0.7977 (pm20) REVERT: D 345 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: D 359 GLN cc_start: 0.8217 (tp40) cc_final: 0.7984 (tt0) REVERT: E 84 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7736 (tt0) REVERT: E 101 HIS cc_start: 0.8717 (m90) cc_final: 0.8226 (m-70) REVERT: E 125 ARG cc_start: 0.9133 (mtt180) cc_final: 0.8787 (ttp80) REVERT: E 152 HIS cc_start: 0.8330 (t-90) cc_final: 0.8115 (t70) REVERT: E 348 ARG cc_start: 0.5140 (OUTLIER) cc_final: 0.4545 (mtm180) REVERT: E 364 CYS cc_start: 0.6657 (t) cc_final: 0.6031 (t) REVERT: E 376 GLU cc_start: 0.7510 (pm20) cc_final: 0.7116 (pm20) REVERT: F 91 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7924 (mtmm) REVERT: F 100 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: G 32 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8517 (tp40) REVERT: G 122 ASP cc_start: 0.8181 (p0) cc_final: 0.7952 (p0) REVERT: G 124 THR cc_start: 0.9468 (m) cc_final: 0.9255 (p) REVERT: H 38 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.7957 (mtp-110) REVERT: H 47 THR cc_start: 0.8382 (p) cc_final: 0.8014 (p) REVERT: I 66 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8041 (mtm110) REVERT: I 104 GLU cc_start: 0.8443 (tt0) cc_final: 0.7800 (pp20) outliers start: 58 outliers final: 35 residues processed: 216 average time/residue: 1.0543 time to fit residues: 252.7330 Evaluate side-chains 218 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 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 345 GLN 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 77 SER 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 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 Chi-restraints excluded: chain I residue 66 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** I 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.154993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104275 restraints weight = 20461.198| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.26 r_work: 0.3264 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2554 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= 0.129 Angle : 0.592 10.466 17352 Z= 0.291 Chirality : 0.042 0.199 2033 Planarity : 0.004 0.053 2199 Dihedral : 5.165 44.113 2041 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.29 % Allowed : 18.99 % Favored : 76.72 % 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: -0.79 (0.20), residues: 1575 helix: -0.21 (0.40), residues: 153 sheet: -0.60 (0.24), residues: 441 loop : -0.48 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.011 0.001 HIS A 117 PHE 0.011 0.001 PHE E 334 TYR 0.018 0.001 TYR A 81 ARG 0.004 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 8) link_NAG-ASN : angle 2.19491 ( 24) link_ALPHA1-6 : bond 0.00570 ( 2) link_ALPHA1-6 : angle 1.53589 ( 6) link_BETA1-4 : bond 0.00676 ( 5) link_BETA1-4 : angle 2.51662 ( 15) hydrogen bonds : bond 0.03123 ( 368) hydrogen bonds : angle 5.39953 ( 996) SS BOND : bond 0.00227 ( 17) SS BOND : angle 1.15981 ( 34) covalent geometry : bond 0.00305 (12684) covalent geometry : angle 0.57970 (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 228 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8648 (t) REVERT: A 142 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: B 303 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8293 (mmm160) REVERT: B 305 ASP cc_start: 0.8414 (t0) cc_final: 0.8196 (t0) REVERT: B 313 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: B 362 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8304 (mt-10) REVERT: B 378 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7700 (tp40) REVERT: C 126 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7098 (mm-40) REVERT: C 139 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: C 152 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7469 (ttp-110) REVERT: C 233 GLN cc_start: 0.8241 (pm20) cc_final: 0.7943 (pm20) REVERT: D 345 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: D 359 GLN cc_start: 0.8185 (tp40) cc_final: 0.7956 (tt0) REVERT: E 84 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7752 (tt0) REVERT: E 101 HIS cc_start: 0.8721 (m90) cc_final: 0.8220 (m-70) REVERT: E 125 ARG cc_start: 0.9147 (mtt180) cc_final: 0.8816 (ttp80) REVERT: E 152 HIS cc_start: 0.8309 (t-90) cc_final: 0.8097 (t70) REVERT: E 348 ARG cc_start: 0.5087 (OUTLIER) cc_final: 0.4509 (mtm180) REVERT: E 364 CYS cc_start: 0.6624 (t) cc_final: 0.6012 (t) REVERT: E 376 GLU cc_start: 0.7502 (pm20) cc_final: 0.7070 (pm20) REVERT: F 100 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: G 32 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8496 (tp40) REVERT: G 122 ASP cc_start: 0.8157 (p0) cc_final: 0.7917 (p0) REVERT: H 38 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.7666 (mtp-110) REVERT: H 101 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (tm-30) REVERT: I 66 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8101 (mtp-110) outliers start: 56 outliers final: 32 residues processed: 209 average time/residue: 1.4494 time to fit residues: 332.4091 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 : 1.548 ------------------------------------------------------------------------------- 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 345 GLN 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 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 77 SER 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 76 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 101 GLN 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 I residue 22 VAL Chi-restraints excluded: chain I residue 66 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 132 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.155209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104706 restraints weight = 20541.755| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.28 r_work: 0.3269 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2653 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= 0.130 Angle : 0.596 10.560 17352 Z= 0.294 Chirality : 0.042 0.204 2033 Planarity : 0.004 0.051 2199 Dihedral : 4.948 39.386 2041 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.91 % Allowed : 20.06 % Favored : 76.03 % 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: -0.73 (0.20), residues: 1575 helix: -0.10 (0.41), residues: 152 sheet: -0.58 (0.24), residues: 436 loop : -0.44 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.011 0.001 HIS A 117 PHE 0.012 0.001 PHE E 334 TYR 0.018 0.001 TYR A 81 ARG 0.004 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 8) link_NAG-ASN : angle 2.17416 ( 24) link_ALPHA1-6 : bond 0.00575 ( 2) link_ALPHA1-6 : angle 1.52078 ( 6) link_BETA1-4 : bond 0.00694 ( 5) link_BETA1-4 : angle 2.42918 ( 15) hydrogen bonds : bond 0.03094 ( 368) hydrogen bonds : angle 5.35426 ( 996) SS BOND : bond 0.00243 ( 17) SS BOND : angle 1.08226 ( 34) covalent geometry : bond 0.00308 (12684) covalent geometry : angle 0.58527 (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 222 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8632 (t) REVERT: A 142 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: B 305 ASP cc_start: 0.8428 (t0) cc_final: 0.8212 (t0) REVERT: B 313 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: B 362 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 378 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7688 (tp40) REVERT: C 126 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.7069 (mm-40) REVERT: C 139 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: C 152 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7485 (ttp-110) REVERT: C 233 GLN cc_start: 0.8231 (pm20) cc_final: 0.7939 (pm20) REVERT: D 345 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: D 359 GLN cc_start: 0.8169 (tp40) cc_final: 0.7949 (tt0) REVERT: E 84 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7758 (tt0) REVERT: E 101 HIS cc_start: 0.8728 (m90) cc_final: 0.8228 (m-70) REVERT: E 125 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8806 (ttp80) REVERT: E 152 HIS cc_start: 0.8292 (t-90) cc_final: 0.8083 (t70) REVERT: E 348 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4505 (mtm180) REVERT: E 364 CYS cc_start: 0.6401 (t) cc_final: 0.5896 (t) REVERT: E 376 GLU cc_start: 0.7451 (pm20) cc_final: 0.7016 (pm20) REVERT: F 58 GLN cc_start: 0.8678 (tt0) cc_final: 0.8339 (pt0) REVERT: F 100 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: G 22 GLN cc_start: 0.8275 (pp30) cc_final: 0.7768 (pm20) REVERT: G 32 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8493 (tp40) REVERT: G 135 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8044 (pp) REVERT: H 47 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8005 (p) REVERT: H 101 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8832 (tm-30) REVERT: I 66 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8075 (mtp-110) outliers start: 51 outliers final: 27 residues processed: 203 average time/residue: 1.3430 time to fit residues: 302.2297 Evaluate side-chains 202 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 345 GLN 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 184 VAL Chi-restraints excluded: chain E residue 348 ARG 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 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 98 LEU Chi-restraints excluded: chain H residue 101 GLN 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 I residue 22 VAL Chi-restraints excluded: chain I residue 66 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 31 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.155468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105637 restraints weight = 20454.352| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.37 r_work: 0.3283 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12716 Z= 0.134 Angle : 0.608 11.608 17352 Z= 0.298 Chirality : 0.042 0.257 2033 Planarity : 0.004 0.049 2199 Dihedral : 4.845 38.964 2041 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.83 % Allowed : 20.29 % 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: -0.72 (0.20), residues: 1575 helix: -0.07 (0.41), residues: 152 sheet: -0.58 (0.24), residues: 438 loop : -0.43 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 72 HIS 0.012 0.001 HIS A 117 PHE 0.011 0.001 PHE E 334 TYR 0.019 0.001 TYR A 81 ARG 0.004 0.000 ARG B 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 2.15876 ( 24) link_ALPHA1-6 : bond 0.00637 ( 2) link_ALPHA1-6 : angle 1.53391 ( 6) link_BETA1-4 : bond 0.00638 ( 5) link_BETA1-4 : angle 2.35495 ( 15) hydrogen bonds : bond 0.03116 ( 368) hydrogen bonds : angle 5.34227 ( 996) SS BOND : bond 0.00247 ( 17) SS BOND : angle 1.03028 ( 34) covalent geometry : bond 0.00320 (12684) covalent geometry : angle 0.59788 (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: 50 poor density : 160 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: B 305 ASP cc_start: 0.8399 (t0) cc_final: 0.8192 (t0) REVERT: B 313 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: B 362 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8339 (mt-10) REVERT: B 378 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7712 (tp40) REVERT: C 126 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.7042 (mm-40) REVERT: C 139 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8393 (mm-30) REVERT: C 152 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7580 (ttp-110) REVERT: C 233 GLN cc_start: 0.8204 (pm20) cc_final: 0.7931 (pm20) REVERT: D 359 GLN cc_start: 0.8240 (tp40) cc_final: 0.8019 (tt0) REVERT: E 84 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7736 (tt0) REVERT: E 101 HIS cc_start: 0.8629 (m90) cc_final: 0.8124 (m-70) REVERT: E 125 ARG cc_start: 0.9080 (mtt180) cc_final: 0.8796 (ttp80) REVERT: E 348 ARG cc_start: 0.5302 (OUTLIER) cc_final: 0.4674 (mtm180) REVERT: E 364 CYS cc_start: 0.6553 (t) cc_final: 0.6060 (t) REVERT: E 376 GLU cc_start: 0.7439 (pm20) cc_final: 0.6971 (pm20) REVERT: F 58 GLN cc_start: 0.8701 (tt0) cc_final: 0.8373 (pt0) REVERT: F 100 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: G 22 GLN cc_start: 0.8335 (pp30) cc_final: 0.7826 (pm20) REVERT: G 32 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8445 (tp40) REVERT: G 135 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8098 (pp) REVERT: H 47 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8107 (p) REVERT: I 66 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8106 (mtp-110) outliers start: 50 outliers final: 30 residues processed: 195 average time/residue: 1.2330 time to fit residues: 263.5136 Evaluate side-chains 199 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain E residue 348 ARG 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 71 ARG 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 I residue 22 VAL Chi-restraints excluded: chain I residue 66 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 20.0000 chunk 38 optimal weight: 0.0570 chunk 80 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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** I 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.156170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106827 restraints weight = 20551.764| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.36 r_work: 0.3295 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12716 Z= 0.118 Angle : 0.600 12.407 17352 Z= 0.294 Chirality : 0.042 0.231 2033 Planarity : 0.004 0.050 2199 Dihedral : 4.673 37.601 2041 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.29 % Allowed : 20.67 % Favored : 76.03 % 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: -0.71 (0.20), residues: 1575 helix: -0.09 (0.41), residues: 153 sheet: -0.56 (0.24), residues: 436 loop : -0.42 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 72 HIS 0.008 0.001 HIS A 117 PHE 0.011 0.001 PHE E 334 TYR 0.017 0.001 TYR A 81 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 8) link_NAG-ASN : angle 2.09808 ( 24) link_ALPHA1-6 : bond 0.00595 ( 2) link_ALPHA1-6 : angle 1.47740 ( 6) link_BETA1-4 : bond 0.00702 ( 5) link_BETA1-4 : angle 2.26040 ( 15) hydrogen bonds : bond 0.03021 ( 368) hydrogen bonds : angle 5.32029 ( 996) SS BOND : bond 0.00232 ( 17) SS BOND : angle 0.92435 ( 34) covalent geometry : bond 0.00280 (12684) covalent geometry : angle 0.59084 (17273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11730.75 seconds wall clock time: 207 minutes 31.13 seconds (12451.13 seconds total)