Starting phenix.real_space_refine on Thu Sep 18 00:09:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rew_19110/09_2025/8rew_19110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rew_19110/09_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_19110/09_2025/8rew_19110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rew_19110/09_2025/8rew_19110.map" model { file = "/net/cci-nas-00/data/ceres_data/8rew_19110/09_2025/8rew_19110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rew_19110/09_2025/8rew_19110.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASP:plan': 3, 'ARG:plan': 2} 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: {'HIS:plan': 2, 'ARG:plan': 14, 'GLN:plan1': 3, 'GLU:plan': 5} 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: 2.88, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 545.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.36 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: 1.92 Time building geometry restraints manager: 1.39 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 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: 5.870 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.930 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (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 ARG 0.015 0.001 ARG A 43 TYR 0.020 0.002 TYR G 129 PHE 0.028 0.002 PHE H 48 TRP 0.018 0.001 TRP B 310 HIS 0.013 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00440 (12684) covalent geometry : angle 0.82700 (17273) SS BOND : bond 0.00224 ( 17) SS BOND : angle 1.17398 ( 34) hydrogen bonds : bond 0.15458 ( 368) hydrogen bonds : angle 7.52105 ( 996) 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) link_NAG-ASN : bond 0.00334 ( 8) link_NAG-ASN : angle 2.34338 ( 24) *********************** 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 : 0.482 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: 0.5622 time to fit residues: 162.0524 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 : 0.469 ------------------------------------------------------------------------------- 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 98 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 201 HIS ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 ASN I 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.155909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105306 restraints weight = 20193.083| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.55 r_work: 0.3272 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12716 Z= 0.189 Angle : 0.637 9.065 17352 Z= 0.320 Chirality : 0.043 0.188 2033 Planarity : 0.005 0.079 2199 Dihedral : 8.525 78.986 2046 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.20), residues: 1575 helix: -0.80 (0.39), residues: 148 sheet: -0.56 (0.24), residues: 453 loop : -0.54 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 421 TYR 0.018 0.002 TYR H 99 PHE 0.031 0.002 PHE H 48 TRP 0.012 0.001 TRP B 310 HIS 0.007 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00443 (12684) covalent geometry : angle 0.62651 (17273) SS BOND : bond 0.00367 ( 17) SS BOND : angle 1.13074 ( 34) hydrogen bonds : bond 0.04216 ( 368) hydrogen bonds : angle 6.15351 ( 996) link_ALPHA1-6 : bond 0.00491 ( 2) link_ALPHA1-6 : angle 1.90708 ( 6) link_BETA1-4 : bond 0.00575 ( 5) link_BETA1-4 : angle 2.03339 ( 15) link_NAG-ASN : bond 0.00401 ( 8) link_NAG-ASN : angle 2.28048 ( 24) *********************** 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 233 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6706 (pp20) REVERT: A 128 THR cc_start: 0.9095 (p) cc_final: 0.8671 (t) REVERT: C 126 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6471 (mp10) REVERT: C 139 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: D 345 GLN cc_start: 0.8164 (pm20) cc_final: 0.7915 (pm20) REVERT: E 101 HIS cc_start: 0.8714 (m-70) cc_final: 0.8213 (m-70) REVERT: E 196 LEU cc_start: 0.7278 (mt) cc_final: 0.7036 (mp) REVERT: E 338 LEU cc_start: 0.8208 (tm) cc_final: 0.7988 (tm) REVERT: E 376 GLU cc_start: 0.7395 (pm20) cc_final: 0.7100 (pm20) REVERT: F 91 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7952 (mtmm) REVERT: F 113 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7564 (pmm) REVERT: G 32 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8618 (mm110) outliers start: 39 outliers final: 16 residues processed: 212 average time/residue: 0.5055 time to fit residues: 118.0848 Evaluate side-chains 183 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 24 VAL 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 133 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 297 GLN ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096574 restraints weight = 20699.875| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.37 r_work: 0.3130 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 12716 Z= 0.447 Angle : 0.812 7.906 17352 Z= 0.408 Chirality : 0.050 0.339 2033 Planarity : 0.006 0.066 2199 Dihedral : 8.186 67.714 2041 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.11 % Rotamer: Outliers : 5.82 % Allowed : 14.01 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.20), residues: 1575 helix: -0.86 (0.38), residues: 160 sheet: -0.63 (0.25), residues: 434 loop : -0.76 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 121 TYR 0.020 0.003 TYR D 317 PHE 0.057 0.003 PHE H 48 TRP 0.019 0.003 TRP G 130 HIS 0.007 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.01051 (12684) covalent geometry : angle 0.79825 (17273) SS BOND : bond 0.00592 ( 17) SS BOND : angle 1.88999 ( 34) hydrogen bonds : bond 0.05008 ( 368) hydrogen bonds : angle 6.33245 ( 996) link_ALPHA1-6 : bond 0.01012 ( 2) link_ALPHA1-6 : angle 2.21183 ( 6) link_BETA1-4 : bond 0.00284 ( 5) link_BETA1-4 : angle 2.00166 ( 15) link_NAG-ASN : bond 0.00937 ( 8) link_NAG-ASN : angle 2.99549 ( 24) *********************** 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 262 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 186 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: A 142 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: B 292 ASN cc_start: 0.8371 (m110) cc_final: 0.8111 (m-40) REVERT: B 313 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: B 377 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: B 378 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: C 126 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: C 152 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7443 (ttp-110) REVERT: D 359 GLN cc_start: 0.8277 (tp40) cc_final: 0.7889 (tt0) REVERT: E 84 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7708 (tt0) REVERT: E 101 HIS cc_start: 0.8656 (m-70) cc_final: 0.8133 (m-70) REVERT: E 125 ARG cc_start: 0.9122 (mtt180) cc_final: 0.8853 (ttp80) REVERT: E 196 LEU cc_start: 0.7513 (mt) cc_final: 0.7251 (mp) REVERT: E 338 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7706 (tp) REVERT: E 348 ARG cc_start: 0.5547 (OUTLIER) cc_final: 0.4976 (mtm180) REVERT: E 376 GLU cc_start: 0.7529 (pm20) cc_final: 0.7080 (pm20) REVERT: F 91 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8075 (mtmm) REVERT: F 100 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: G 32 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8633 (mm110) REVERT: H 21 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7721 (tp) REVERT: H 47 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8241 (p) REVERT: I 104 GLU cc_start: 0.8523 (tt0) cc_final: 0.7832 (pp20) outliers start: 76 outliers final: 29 residues processed: 230 average time/residue: 0.5309 time to fit residues: 134.0628 Evaluate side-chains 211 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 377 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain C residue 64 SER 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 D residue 379 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 338 LEU 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 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 21 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 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 109 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 143 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 177 ASN C 117 HIS ** C 184 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.153496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102617 restraints weight = 20293.643| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.51 r_work: 0.3220 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12716 Z= 0.132 Angle : 0.623 11.699 17352 Z= 0.309 Chirality : 0.043 0.288 2033 Planarity : 0.004 0.060 2199 Dihedral : 7.125 56.940 2041 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.90 % Allowed : 16.69 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.20), residues: 1575 helix: -0.50 (0.40), residues: 154 sheet: -0.59 (0.24), residues: 433 loop : -0.64 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 121 TYR 0.014 0.001 TYR A 171 PHE 0.016 0.001 PHE E 334 TRP 0.016 0.001 TRP E 247 HIS 0.006 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00301 (12684) covalent geometry : angle 0.61039 (17273) SS BOND : bond 0.00288 ( 17) SS BOND : angle 1.29206 ( 34) hydrogen bonds : bond 0.03490 ( 368) hydrogen bonds : angle 5.94797 ( 996) link_ALPHA1-6 : bond 0.00667 ( 2) link_ALPHA1-6 : angle 1.59508 ( 6) link_BETA1-4 : bond 0.00437 ( 5) link_BETA1-4 : angle 2.21241 ( 15) link_NAG-ASN : bond 0.00341 ( 8) link_NAG-ASN : angle 2.60990 ( 24) *********************** 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 249 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6587 (pp20) REVERT: A 128 THR cc_start: 0.9110 (p) cc_final: 0.8694 (t) REVERT: A 142 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: B 305 ASP cc_start: 0.8471 (t70) cc_final: 0.8202 (t0) REVERT: B 313 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8601 (mp0) REVERT: B 362 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 119 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8232 (pt0) REVERT: C 126 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6476 (mp10) REVERT: C 152 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.7466 (ttp-110) REVERT: C 185 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7454 (mpt-90) REVERT: D 359 GLN cc_start: 0.8211 (tp40) cc_final: 0.7910 (tt0) REVERT: E 84 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7712 (tt0) REVERT: E 101 HIS cc_start: 0.8614 (m-70) cc_final: 0.8064 (m-70) REVERT: E 338 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7892 (tp) REVERT: E 364 CYS cc_start: 0.6751 (t) cc_final: 0.6096 (t) REVERT: E 376 GLU cc_start: 0.7497 (pm20) cc_final: 0.7071 (pm20) REVERT: F 100 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: G 32 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8623 (mm110) REVERT: G 53 MET cc_start: 0.8965 (mmt) cc_final: 0.8419 (mmt) REVERT: G 101 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8210 (tm-30) REVERT: G 124 THR cc_start: 0.9483 (m) cc_final: 0.9170 (p) REVERT: G 134 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7927 (p) REVERT: H 32 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8120 (mp10) REVERT: H 38 ARG cc_start: 0.8550 (tpt-90) cc_final: 0.8270 (tpp-160) REVERT: H 47 THR cc_start: 0.8421 (p) cc_final: 0.8123 (p) outliers start: 64 outliers final: 21 residues processed: 230 average time/residue: 0.5067 time to fit residues: 128.1464 Evaluate side-chains 200 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 313 GLU 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 185 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 184 VAL Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 338 LEU 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 134 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 88 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 98 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.153089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102543 restraints weight = 20613.470| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.49 r_work: 0.3215 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12716 Z= 0.166 Angle : 0.620 8.857 17352 Z= 0.308 Chirality : 0.043 0.222 2033 Planarity : 0.004 0.055 2199 Dihedral : 6.614 52.536 2041 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.52 % Allowed : 18.45 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1575 helix: -0.10 (0.42), residues: 147 sheet: -0.73 (0.24), residues: 437 loop : -0.56 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 125 TYR 0.026 0.002 TYR A 81 PHE 0.013 0.001 PHE E 334 TRP 0.011 0.001 TRP B 310 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00393 (12684) covalent geometry : angle 0.60773 (17273) SS BOND : bond 0.00345 ( 17) SS BOND : angle 1.23247 ( 34) hydrogen bonds : bond 0.03492 ( 368) hydrogen bonds : angle 5.81765 ( 996) link_ALPHA1-6 : bond 0.00580 ( 2) link_ALPHA1-6 : angle 1.65212 ( 6) link_BETA1-4 : bond 0.00494 ( 5) link_BETA1-4 : angle 2.39660 ( 15) link_NAG-ASN : bond 0.00364 ( 8) link_NAG-ASN : angle 2.45982 ( 24) *********************** 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 241 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 107 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6644 (pp20) REVERT: A 128 THR cc_start: 0.9116 (p) cc_final: 0.8719 (t) REVERT: A 142 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 305 ASP cc_start: 0.8500 (t70) cc_final: 0.8198 (t0) REVERT: B 313 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8612 (mp0) REVERT: B 362 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8356 (mt-10) REVERT: C 126 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6523 (mp10) REVERT: C 152 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7471 (ttp-110) REVERT: C 177 ASN cc_start: 0.8780 (t0) cc_final: 0.8573 (m-40) REVERT: C 185 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7432 (mpt-90) REVERT: D 345 GLN cc_start: 0.8338 (pm20) cc_final: 0.7861 (pm20) REVERT: D 359 GLN cc_start: 0.8198 (tp40) cc_final: 0.7918 (tt0) REVERT: E 84 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7760 (tt0) REVERT: E 101 HIS cc_start: 0.8612 (m-70) cc_final: 0.8088 (m-70) REVERT: E 152 HIS cc_start: 0.8410 (t-90) cc_final: 0.8191 (t70) REVERT: E 338 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7913 (tp) REVERT: E 364 CYS cc_start: 0.6689 (t) cc_final: 0.6071 (t) REVERT: E 376 GLU cc_start: 0.7513 (pm20) cc_final: 0.7018 (pm20) REVERT: F 100 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: G 32 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8632 (mm110) REVERT: G 101 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8202 (tm-30) REVERT: G 122 ASP cc_start: 0.8358 (p0) cc_final: 0.8121 (p0) REVERT: G 124 THR cc_start: 0.9487 (m) cc_final: 0.9230 (p) REVERT: H 32 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8112 (mp10) REVERT: H 38 ARG cc_start: 0.8558 (tpt-90) cc_final: 0.8258 (tpp-160) REVERT: H 47 THR cc_start: 0.8400 (p) cc_final: 0.8054 (p) outliers start: 59 outliers final: 27 residues processed: 222 average time/residue: 0.5070 time to fit residues: 124.3701 Evaluate side-chains 208 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain B residue 293 CYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 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 327 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 556 MET 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 134 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 151 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 127 optimal weight: 0.0870 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ** C 184 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 = 0.4114 r_free = 0.4114 target = 0.154385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104671 restraints weight = 20438.388| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.37 r_work: 0.3247 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2498 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= 0.130 Angle : 0.599 8.704 17352 Z= 0.296 Chirality : 0.042 0.204 2033 Planarity : 0.004 0.055 2199 Dihedral : 6.014 50.889 2041 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.29 % Allowed : 19.91 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.20), residues: 1575 helix: -0.17 (0.42), residues: 151 sheet: -0.71 (0.24), residues: 435 loop : -0.55 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 125 TYR 0.024 0.001 TYR A 81 PHE 0.012 0.001 PHE E 334 TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00306 (12684) covalent geometry : angle 0.58689 (17273) SS BOND : bond 0.00266 ( 17) SS BOND : angle 1.10701 ( 34) hydrogen bonds : bond 0.03229 ( 368) hydrogen bonds : angle 5.65314 ( 996) link_ALPHA1-6 : bond 0.00596 ( 2) link_ALPHA1-6 : angle 1.57984 ( 6) link_BETA1-4 : bond 0.00601 ( 5) link_BETA1-4 : angle 2.47982 ( 15) link_NAG-ASN : bond 0.00311 ( 8) link_NAG-ASN : angle 2.27435 ( 24) *********************** 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 234 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: A 128 THR cc_start: 0.9087 (p) cc_final: 0.8710 (t) REVERT: A 142 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: B 305 ASP cc_start: 0.8502 (t70) cc_final: 0.8130 (t0) REVERT: B 362 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 126 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: C 139 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8260 (mm-30) REVERT: C 152 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7467 (ttp-110) REVERT: C 177 ASN cc_start: 0.8744 (t0) cc_final: 0.8526 (m-40) REVERT: C 185 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7328 (ttm170) REVERT: D 345 GLN cc_start: 0.8283 (pm20) cc_final: 0.7804 (pm20) REVERT: D 359 GLN cc_start: 0.8186 (tp40) cc_final: 0.7937 (tt0) REVERT: E 84 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7770 (tt0) REVERT: E 101 HIS cc_start: 0.8660 (m-70) cc_final: 0.8123 (m90) REVERT: E 152 HIS cc_start: 0.8428 (t-90) cc_final: 0.8217 (t70) REVERT: E 338 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7905 (tp) REVERT: E 364 CYS cc_start: 0.6607 (t) cc_final: 0.5983 (t) REVERT: E 376 GLU cc_start: 0.7478 (pm20) cc_final: 0.7004 (pm20) REVERT: F 91 LYS cc_start: 0.8265 (mtpp) cc_final: 0.8019 (mtmm) REVERT: G 32 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8614 (mm110) REVERT: G 53 MET cc_start: 0.8966 (mmt) cc_final: 0.8583 (mmt) REVERT: G 101 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8182 (tm-30) REVERT: G 122 ASP cc_start: 0.8308 (p0) cc_final: 0.8085 (p0) REVERT: G 124 THR cc_start: 0.9459 (m) cc_final: 0.9233 (p) REVERT: H 32 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8083 (mp10) REVERT: H 38 ARG cc_start: 0.8478 (tpt-90) cc_final: 0.8235 (tpp-160) REVERT: H 47 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8029 (p) outliers start: 56 outliers final: 28 residues processed: 215 average time/residue: 0.5040 time to fit residues: 119.3023 Evaluate side-chains 205 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 185 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 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 338 LEU Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain F residue 77 SER 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 134 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 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 119 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 112 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 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 = 0.4091 r_free = 0.4091 target = 0.152461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102195 restraints weight = 20466.660| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.43 r_work: 0.3211 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12716 Z= 0.195 Angle : 0.629 7.981 17352 Z= 0.312 Chirality : 0.043 0.228 2033 Planarity : 0.004 0.053 2199 Dihedral : 5.762 49.951 2041 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.75 % Allowed : 19.98 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1575 helix: -0.18 (0.41), residues: 154 sheet: -0.77 (0.24), residues: 442 loop : -0.55 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 125 TYR 0.024 0.002 TYR A 81 PHE 0.013 0.001 PHE G 48 TRP 0.012 0.001 TRP G 66 HIS 0.005 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00462 (12684) covalent geometry : angle 0.61671 (17273) SS BOND : bond 0.00349 ( 17) SS BOND : angle 1.14572 ( 34) hydrogen bonds : bond 0.03492 ( 368) hydrogen bonds : angle 5.63464 ( 996) link_ALPHA1-6 : bond 0.00708 ( 2) link_ALPHA1-6 : angle 1.67270 ( 6) link_BETA1-4 : bond 0.00567 ( 5) link_BETA1-4 : angle 2.58550 ( 15) link_NAG-ASN : bond 0.00371 ( 8) link_NAG-ASN : angle 2.36713 ( 24) *********************** 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 242 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 180 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6678 (pp20) REVERT: A 128 THR cc_start: 0.9091 (p) cc_final: 0.8712 (t) REVERT: A 142 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 305 ASP cc_start: 0.8524 (t70) cc_final: 0.8175 (t0) REVERT: B 309 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8329 (mmtp) REVERT: B 362 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8296 (mt-10) REVERT: C 126 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6527 (mp10) REVERT: C 139 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8285 (mm-30) REVERT: C 152 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7470 (ttp-110) REVERT: C 177 ASN cc_start: 0.8797 (t0) cc_final: 0.8577 (m110) REVERT: C 185 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7486 (mpt-90) REVERT: C 233 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: D 345 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: D 359 GLN cc_start: 0.8187 (tp40) cc_final: 0.7908 (tt0) REVERT: E 84 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7766 (tt0) REVERT: E 101 HIS cc_start: 0.8657 (m-70) cc_final: 0.8128 (m-70) REVERT: E 152 HIS cc_start: 0.8459 (t-90) cc_final: 0.8259 (t70) REVERT: E 338 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7821 (tp) REVERT: E 364 CYS cc_start: 0.6616 (t) cc_final: 0.5965 (t) REVERT: E 376 GLU cc_start: 0.7456 (pm20) cc_final: 0.6973 (pm20) REVERT: F 91 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8018 (mtmm) REVERT: G 22 GLN cc_start: 0.8285 (pp30) cc_final: 0.7813 (pm20) REVERT: G 32 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8613 (mm110) REVERT: G 101 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8159 (tm-30) REVERT: G 122 ASP cc_start: 0.8267 (p0) cc_final: 0.8017 (p0) REVERT: G 124 THR cc_start: 0.9488 (m) cc_final: 0.9241 (p) REVERT: H 32 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8087 (mp10) REVERT: H 38 ARG cc_start: 0.8528 (tpt-90) cc_final: 0.8263 (tpp-160) REVERT: H 47 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8025 (p) outliers start: 62 outliers final: 35 residues processed: 220 average time/residue: 0.4926 time to fit residues: 119.5992 Evaluate side-chains 217 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 233 GLN 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 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 167 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 137 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 111 optimal weight: 40.0000 chunk 141 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4108 r_free = 0.4108 target = 0.153700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104860 restraints weight = 20423.098| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.28 r_work: 0.3244 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12716 Z= 0.149 Angle : 0.623 9.947 17352 Z= 0.306 Chirality : 0.043 0.210 2033 Planarity : 0.004 0.054 2199 Dihedral : 5.499 48.004 2041 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.52 % Allowed : 20.21 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.20), residues: 1575 helix: -0.18 (0.41), residues: 154 sheet: -0.67 (0.24), residues: 432 loop : -0.52 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 121 TYR 0.023 0.001 TYR A 81 PHE 0.011 0.001 PHE C 217 TRP 0.011 0.001 TRP H 66 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00350 (12684) covalent geometry : angle 0.61127 (17273) SS BOND : bond 0.00263 ( 17) SS BOND : angle 1.01922 ( 34) hydrogen bonds : bond 0.03256 ( 368) hydrogen bonds : angle 5.57089 ( 996) link_ALPHA1-6 : bond 0.00701 ( 2) link_ALPHA1-6 : angle 1.58445 ( 6) link_BETA1-4 : bond 0.00662 ( 5) link_BETA1-4 : angle 2.58067 ( 15) link_NAG-ASN : bond 0.00303 ( 8) link_NAG-ASN : angle 2.27513 ( 24) *********************** 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 234 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 THR cc_start: 0.9075 (p) cc_final: 0.8698 (t) REVERT: A 142 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: B 305 ASP cc_start: 0.8527 (t70) cc_final: 0.8139 (t0) REVERT: B 309 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8403 (mmtp) REVERT: B 362 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8250 (mt-10) REVERT: C 126 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6500 (mp10) REVERT: C 139 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: C 152 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7470 (ttp-110) REVERT: C 185 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7469 (mpt-90) REVERT: C 233 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: D 345 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: D 359 GLN cc_start: 0.8136 (tp40) cc_final: 0.7903 (tt0) REVERT: E 101 HIS cc_start: 0.8612 (m-70) cc_final: 0.8076 (m-70) REVERT: E 152 HIS cc_start: 0.8459 (t-90) cc_final: 0.8247 (t70) REVERT: E 338 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7857 (tp) REVERT: E 364 CYS cc_start: 0.6604 (t) cc_final: 0.5914 (t) REVERT: E 376 GLU cc_start: 0.7437 (pm20) cc_final: 0.6967 (pm20) REVERT: F 91 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7952 (mtmm) REVERT: F 100 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: G 22 GLN cc_start: 0.8284 (pp30) cc_final: 0.7804 (pm20) REVERT: G 32 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8506 (tp40) REVERT: G 101 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8175 (tm-30) REVERT: G 122 ASP cc_start: 0.8186 (p0) cc_final: 0.7924 (p0) REVERT: G 124 THR cc_start: 0.9479 (m) cc_final: 0.9221 (p) REVERT: H 32 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7995 (mp10) REVERT: H 47 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7875 (p) outliers start: 59 outliers final: 33 residues processed: 213 average time/residue: 0.5087 time to fit residues: 119.4211 Evaluate side-chains 210 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 126 GLN Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 233 GLN 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 167 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 122 VAL 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 134 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 110 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 49 optimal weight: 6.9990 chunk 142 optimal weight: 0.5980 chunk 141 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 0.0000 chunk 99 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 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 = 0.4116 r_free = 0.4116 target = 0.154436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.104854 restraints weight = 20573.586| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.17 r_work: 0.3258 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12716 Z= 0.134 Angle : 0.615 9.257 17352 Z= 0.302 Chirality : 0.042 0.206 2033 Planarity : 0.004 0.051 2199 Dihedral : 5.223 45.196 2041 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.83 % Allowed : 21.21 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.20), residues: 1575 helix: -0.15 (0.41), residues: 154 sheet: -0.65 (0.24), residues: 428 loop : -0.49 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 125 TYR 0.021 0.001 TYR A 81 PHE 0.011 0.001 PHE C 217 TRP 0.011 0.001 TRP E 247 HIS 0.003 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00318 (12684) covalent geometry : angle 0.60406 (17273) SS BOND : bond 0.00248 ( 17) SS BOND : angle 0.96845 ( 34) hydrogen bonds : bond 0.03182 ( 368) hydrogen bonds : angle 5.49860 ( 996) link_ALPHA1-6 : bond 0.00676 ( 2) link_ALPHA1-6 : angle 1.55060 ( 6) link_BETA1-4 : bond 0.00709 ( 5) link_BETA1-4 : angle 2.51596 ( 15) link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 2.22212 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 128 THR cc_start: 0.9053 (p) cc_final: 0.8688 (t) REVERT: A 142 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: B 303 ARG cc_start: 0.7614 (tpm170) cc_final: 0.7368 (tpm170) REVERT: B 305 ASP cc_start: 0.8498 (t70) cc_final: 0.8104 (t0) REVERT: B 309 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8121 (mmtm) REVERT: B 362 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8248 (mt-10) REVERT: C 139 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8255 (mm-30) REVERT: C 152 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7449 (ttp-110) REVERT: C 185 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7288 (ttm170) REVERT: C 233 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: D 345 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8059 (pm20) REVERT: D 359 GLN cc_start: 0.8130 (tp40) cc_final: 0.7888 (tt0) REVERT: D 375 LYS cc_start: 0.7893 (mttt) cc_final: 0.7501 (mtpt) REVERT: E 84 GLU cc_start: 0.7918 (mp0) cc_final: 0.7298 (tt0) REVERT: E 101 HIS cc_start: 0.8713 (m-70) cc_final: 0.8181 (m-70) REVERT: E 152 HIS cc_start: 0.8403 (t-90) cc_final: 0.8180 (t70) REVERT: E 338 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7742 (tp) REVERT: E 364 CYS cc_start: 0.6455 (t) cc_final: 0.5794 (t) REVERT: E 376 GLU cc_start: 0.7389 (pm20) cc_final: 0.6961 (pm20) REVERT: F 91 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7968 (mtmm) REVERT: G 22 GLN cc_start: 0.8295 (pp30) cc_final: 0.7811 (pm20) REVERT: G 32 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8519 (tp40) REVERT: G 53 MET cc_start: 0.9000 (mmt) cc_final: 0.8767 (mmt) REVERT: G 101 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8141 (tm-30) REVERT: G 122 ASP cc_start: 0.8172 (p0) cc_final: 0.7910 (p0) REVERT: G 124 THR cc_start: 0.9489 (m) cc_final: 0.9240 (p) REVERT: H 32 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8016 (mp10) REVERT: H 47 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7907 (p) outliers start: 50 outliers final: 26 residues processed: 207 average time/residue: 0.5254 time to fit residues: 119.4280 Evaluate side-chains 204 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 233 GLN 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 364 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 167 HIS Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 135 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 110 THR Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 133 optimal weight: 0.0570 chunk 64 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 80 optimal weight: 0.9980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 177 ASN ** C 184 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** I 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.155772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107962 restraints weight = 20448.572| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.32 r_work: 0.3300 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12716 Z= 0.119 Angle : 0.610 10.160 17352 Z= 0.301 Chirality : 0.042 0.265 2033 Planarity : 0.004 0.053 2199 Dihedral : 4.950 39.332 2041 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.14 % Allowed : 21.90 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.20), residues: 1575 helix: -0.12 (0.41), residues: 154 sheet: -0.63 (0.24), residues: 428 loop : -0.48 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 125 TYR 0.019 0.001 TYR A 81 PHE 0.010 0.001 PHE E 334 TRP 0.012 0.001 TRP H 72 HIS 0.004 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00281 (12684) covalent geometry : angle 0.60047 (17273) SS BOND : bond 0.00221 ( 17) SS BOND : angle 0.90241 ( 34) hydrogen bonds : bond 0.03079 ( 368) hydrogen bonds : angle 5.42325 ( 996) link_ALPHA1-6 : bond 0.00601 ( 2) link_ALPHA1-6 : angle 1.49948 ( 6) link_BETA1-4 : bond 0.00695 ( 5) link_BETA1-4 : angle 2.38176 ( 15) link_NAG-ASN : bond 0.00304 ( 8) link_NAG-ASN : angle 2.14496 ( 24) ********************** 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 218 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.486 Fit side-chains REVERT: A 128 THR cc_start: 0.9036 (p) cc_final: 0.8693 (t) REVERT: A 142 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: B 305 ASP cc_start: 0.8476 (t70) cc_final: 0.8093 (t0) REVERT: B 362 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8322 (mt-10) REVERT: C 139 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8314 (mm-30) REVERT: C 152 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7591 (ttp-110) REVERT: C 185 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7270 (mpt-90) REVERT: C 233 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: D 345 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: D 359 GLN cc_start: 0.8182 (tp40) cc_final: 0.7962 (tt0) REVERT: E 101 HIS cc_start: 0.8554 (m-70) cc_final: 0.7987 (m-70) REVERT: E 125 ARG cc_start: 0.7941 (tmm-80) cc_final: 0.7728 (ttp80) REVERT: E 152 HIS cc_start: 0.8420 (t-90) cc_final: 0.8215 (t70) REVERT: E 364 CYS cc_start: 0.6644 (t) cc_final: 0.5995 (t) REVERT: E 376 GLU cc_start: 0.7387 (pm20) cc_final: 0.6896 (pm20) REVERT: G 22 GLN cc_start: 0.8329 (pp30) cc_final: 0.7857 (pm20) REVERT: G 32 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8493 (tp40) REVERT: G 53 MET cc_start: 0.9019 (mmt) cc_final: 0.8800 (mmt) REVERT: G 101 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8234 (tm-30) REVERT: H 32 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7970 (mp10) REVERT: H 47 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7909 (p) outliers start: 41 outliers final: 22 residues processed: 202 average time/residue: 0.5077 time to fit residues: 112.9978 Evaluate side-chains 195 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE 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 139 GLU Chi-restraints excluded: chain C residue 152 ARG Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 233 GLN 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 184 VAL Chi-restraints excluded: chain E residue 556 MET Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 76 THR 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 47 THR Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 119 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.155493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105923 restraints weight = 20472.632| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.46 r_work: 0.3281 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2914 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= 0.129 Angle : 0.619 11.347 17352 Z= 0.304 Chirality : 0.042 0.230 2033 Planarity : 0.004 0.052 2199 Dihedral : 4.822 38.242 2041 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.76 % Allowed : 22.59 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1575 helix: -0.10 (0.41), residues: 154 sheet: -0.61 (0.24), residues: 436 loop : -0.43 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 125 TYR 0.019 0.001 TYR A 81 PHE 0.010 0.001 PHE C 217 TRP 0.012 0.001 TRP H 72 HIS 0.011 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00308 (12684) covalent geometry : angle 0.60976 (17273) SS BOND : bond 0.00245 ( 17) SS BOND : angle 0.94033 ( 34) hydrogen bonds : bond 0.03119 ( 368) hydrogen bonds : angle 5.38128 ( 996) link_ALPHA1-6 : bond 0.00528 ( 2) link_ALPHA1-6 : angle 1.47254 ( 6) link_BETA1-4 : bond 0.00678 ( 5) link_BETA1-4 : angle 2.29680 ( 15) link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 2.14230 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5194.95 seconds wall clock time: 89 minutes 16.56 seconds (5356.56 seconds total)