Starting phenix.real_space_refine on Tue Dec 31 21:15:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuz_35734/12_2024/8iuz_35734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuz_35734/12_2024/8iuz_35734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuz_35734/12_2024/8iuz_35734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuz_35734/12_2024/8iuz_35734.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuz_35734/12_2024/8iuz_35734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuz_35734/12_2024/8iuz_35734.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 87 5.16 5 C 10413 2.51 5 N 2892 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16692 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3782 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: D, G, F, I, E, H Time building chain proxies: 10.84, per 1000 atoms: 0.65 Number of scatterers: 16692 At special positions: 0 Unit cell: (154.944, 150.64, 150.64, 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 87 16.00 O 3300 8.00 N 2892 7.00 C 10413 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 463 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 269 " distance=2.02 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 130 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 297 " distance=2.02 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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=3, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 408 " " NAG A 502 " - " ASN A 29 " " NAG A 503 " - " ASN A 480 " " NAG D 501 " - " ASN D 408 " " NAG D 502 " - " ASN D 29 " " NAG D 503 " - " ASN D 480 " " NAG G 501 " - " ASN G 408 " " NAG G 502 " - " ASN G 29 " " NAG G 503 " - " ASN G 480 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 2.2 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3870 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 57 sheets defined 16.6% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.521A pdb=" N LEU A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.583A pdb=" N LYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 452 removed outlier: 3.628A pdb=" N VAL A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 91 " --> pdb=" O THR B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU D 71 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.520A pdb=" N LEU D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.584A pdb=" N LYS D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 452 removed outlier: 3.628A pdb=" N VAL D 406 " --> pdb=" O GLN D 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 432 " --> pdb=" O MET D 428 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 435 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 437 " --> pdb=" O THR D 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE D 478 " --> pdb=" O CYS D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 91 " --> pdb=" O THR E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.854A pdb=" N THR G 60 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 removed outlier: 3.992A pdb=" N LEU G 71 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 103 removed outlier: 3.520A pdb=" N LEU G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.583A pdb=" N LYS G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 382 removed outlier: 3.901A pdb=" N ASP G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 452 removed outlier: 3.629A pdb=" N VAL G 406 " --> pdb=" O GLN G 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU G 423 " --> pdb=" O SER G 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS G 432 " --> pdb=" O MET G 428 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 434 " --> pdb=" O ASN G 430 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP G 435 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA G 437 " --> pdb=" O THR G 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET G 441 " --> pdb=" O ALA G 437 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 444 " --> pdb=" O GLU G 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 449 " --> pdb=" O TYR G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 473 through 478 removed outlier: 3.530A pdb=" N ILE G 478 " --> pdb=" O CYS G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 488 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.700A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.175A pdb=" N ILE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY A 359 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 354 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR A 348 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=5, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=6, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.860A pdb=" N ILE A 42 " --> pdb=" O ASP A 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE A 259 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 80 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.695A pdb=" N LYS A 92 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP A 226 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 170 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.604A pdb=" N GLU A 112 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.578A pdb=" N LEU A 145 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 156 through 161 Processing sheet with id=12, first strand: chain 'A' and resid 278 through 280 removed outlier: 4.122A pdb=" N CYS A 273 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 294 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU A 457 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 465 " --> pdb=" O GLU A 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=13 Processing sheet with id=14, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN B 3 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 47 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER B 59 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU B 47 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR B 51 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP B 35 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 102 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 90 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY D 359 " --> pdb=" O HIS D 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN D 354 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR D 348 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=23, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=24, first strand: chain 'D' and resid 34 through 35 Processing sheet with id=25, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.861A pdb=" N ILE D 42 " --> pdb=" O ASP D 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=25 Processing sheet with id=26, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE D 259 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU D 80 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.694A pdb=" N LYS D 92 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP D 226 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 170 " --> pdb=" O LEU D 227 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 110 through 113 removed outlier: 3.605A pdb=" N GLU D 112 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'D' and resid 121 through 122 removed outlier: 3.579A pdb=" N LEU D 145 " --> pdb=" O ARG D 122 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'D' and resid 156 through 161 Processing sheet with id=31, first strand: chain 'D' and resid 278 through 280 removed outlier: 4.123A pdb=" N CYS D 273 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 294 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'D' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU D 457 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU D 465 " --> pdb=" O GLU D 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=32 Processing sheet with id=33, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN E 3 " --> pdb=" O THR E 25 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 47 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER E 59 " --> pdb=" O TYR E 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU E 47 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP E 37 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 51 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP E 35 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.749A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 102 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.910A pdb=" N GLY G 359 " --> pdb=" O HIS G 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN G 354 " --> pdb=" O GLY G 357 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.702A pdb=" N TYR G 348 " --> pdb=" O ASP G 363 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=42, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=43, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=44, first strand: chain 'G' and resid 42 through 43 removed outlier: 5.860A pdb=" N ILE G 42 " --> pdb=" O ASP G 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=44 Processing sheet with id=45, first strand: chain 'G' and resid 49 through 51 removed outlier: 3.540A pdb=" N ILE G 259 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU G 80 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'G' and resid 91 through 92 removed outlier: 6.695A pdb=" N LYS G 92 " --> pdb=" O PHE G 224 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N TRP G 226 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 170 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'G' and resid 110 through 113 removed outlier: 3.604A pdb=" N GLU G 112 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.577A pdb=" N LEU G 145 " --> pdb=" O ARG G 122 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'G' and resid 156 through 161 Processing sheet with id=50, first strand: chain 'G' and resid 278 through 280 removed outlier: 4.122A pdb=" N CYS G 273 " --> pdb=" O ILE G 280 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 294 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'G' and resid 456 through 458 removed outlier: 3.592A pdb=" N GLU G 457 " --> pdb=" O GLU G 465 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU G 465 " --> pdb=" O GLU G 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=51 Processing sheet with id=52, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.507A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.576A pdb=" N SER H 59 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.748A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 90 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.656A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1305 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: 6.41 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3819 1.33 - 1.45: 4174 1.45 - 1.58: 8918 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 17037 Sorted by residual: bond pdb=" CB VAL A 235 " pdb=" CG2 VAL A 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.05e+00 bond pdb=" CB VAL G 235 " pdb=" CG2 VAL G 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" CB VAL D 235 " pdb=" CG2 VAL D 235 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.04e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 17032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 22073 2.88 - 5.77: 883 5.77 - 8.65: 88 8.65 - 11.54: 23 11.54 - 14.42: 12 Bond angle restraints: 23079 Sorted by residual: angle pdb=" C ILE I 29 " pdb=" N ASN I 30 " pdb=" CA ASN I 30 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ILE F 29 " pdb=" N ASN F 30 " pdb=" CA ASN F 30 " ideal model delta sigma weight residual 121.54 133.46 -11.92 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C ILE C 29 " pdb=" N ASN C 30 " pdb=" CA ASN C 30 " ideal model delta sigma weight residual 121.54 133.44 -11.90 1.91e+00 2.74e-01 3.88e+01 angle pdb=" N ILE F 29 " pdb=" CA ILE F 29 " pdb=" C ILE F 29 " ideal model delta sigma weight residual 113.71 108.88 4.83 9.50e-01 1.11e+00 2.59e+01 angle pdb=" N ILE I 29 " pdb=" CA ILE I 29 " pdb=" C ILE I 29 " ideal model delta sigma weight residual 113.71 108.89 4.82 9.50e-01 1.11e+00 2.58e+01 ... (remaining 23074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 9254 16.02 - 32.05: 786 32.05 - 48.07: 146 48.07 - 64.09: 29 64.09 - 80.12: 15 Dihedral angle restraints: 10230 sinusoidal: 4164 harmonic: 6066 Sorted by residual: dihedral pdb=" CA ASN G 397 " pdb=" C ASN G 397 " pdb=" N GLU G 398 " pdb=" CA GLU G 398 " ideal model delta harmonic sigma weight residual 180.00 137.42 42.58 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ASN A 397 " pdb=" C ASN A 397 " pdb=" N GLU A 398 " pdb=" CA GLU A 398 " ideal model delta harmonic sigma weight residual 180.00 137.47 42.53 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA ASN D 397 " pdb=" C ASN D 397 " pdb=" N GLU D 398 " pdb=" CA GLU D 398 " ideal model delta harmonic sigma weight residual 180.00 137.53 42.47 0 5.00e+00 4.00e-02 7.21e+01 ... (remaining 10227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2329 0.119 - 0.238: 194 0.238 - 0.358: 21 0.358 - 0.477: 0 0.477 - 0.596: 3 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.88e+00 chirality pdb=" CB ILE D 4 " pdb=" CA ILE D 4 " pdb=" CG1 ILE D 4 " pdb=" CG2 ILE D 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CB ILE G 4 " pdb=" CA ILE G 4 " pdb=" CG1 ILE G 4 " pdb=" CG2 ILE G 4 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.86e+00 ... (remaining 2544 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 143 " -0.025 2.00e-02 2.50e+03 1.97e-02 9.68e+00 pdb=" CG TRP G 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP G 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 143 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP G 143 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " 0.025 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP A 143 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " 0.026 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP D 143 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 3 1.99 - 2.71: 1269 2.71 - 3.44: 21760 3.44 - 4.17: 38588 4.17 - 4.90: 69014 Nonbonded interactions: 130634 Sorted by model distance: nonbonded pdb=" OE1 GLU D 457 " pdb=" NH2 ARG G 453 " model vdw 1.257 3.120 nonbonded pdb=" NH2 ARG A 453 " pdb=" OE1 GLU G 457 " model vdw 1.257 3.120 nonbonded pdb=" OE1 GLU A 457 " pdb=" NH2 ARG D 453 " model vdw 1.257 3.120 nonbonded pdb=" SG CYS D 88 " pdb=" SG CYS D 130 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS D 43 " pdb=" SG CYS D 269 " model vdw 2.024 3.760 ... (remaining 130629 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' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 40.000 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4861 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 : 0.010 0.099 17037 Z= 0.658 Angle : 1.337 14.419 23079 Z= 0.744 Chirality : 0.074 0.596 2547 Planarity : 0.008 0.074 2994 Dihedral : 12.686 80.118 6336 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 0.99 % Allowed : 4.28 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.15), residues: 2103 helix: -3.45 (0.19), residues: 291 sheet: -2.80 (0.18), residues: 663 loop : -2.93 (0.15), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP G 143 HIS 0.013 0.004 HIS D 175 PHE 0.036 0.006 PHE G 335 TYR 0.052 0.004 TYR E 102 ARG 0.020 0.002 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 355 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASN cc_start: 0.8468 (t0) cc_final: 0.8186 (t0) REVERT: B 67 ARG cc_start: 0.6017 (ptp-110) cc_final: 0.5638 (ptt180) REVERT: C 5 ASN cc_start: 0.6169 (m-40) cc_final: 0.5912 (m-40) REVERT: C 50 LYS cc_start: 0.6404 (mttt) cc_final: 0.6195 (mttt) REVERT: D 310 THR cc_start: 0.1801 (OUTLIER) cc_final: 0.1381 (m) REVERT: D 401 LYS cc_start: 0.4301 (mppt) cc_final: 0.4066 (mtmm) REVERT: D 412 ASP cc_start: 0.4848 (t70) cc_final: 0.4625 (t0) REVERT: G 87 VAL cc_start: 0.6014 (m) cc_final: 0.5654 (p) REVERT: G 408 ASN cc_start: 0.4323 (m-40) cc_final: 0.3933 (t160) REVERT: I 67 SER cc_start: 0.2164 (p) cc_final: 0.1766 (m) outliers start: 18 outliers final: 1 residues processed: 368 average time/residue: 1.0877 time to fit residues: 455.0296 Evaluate side-chains 204 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 310 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 156 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 162 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 124 ASN A 155 GLN A 225 HIS A 421 ASN A 430 ASN A 455 ASN A 468 HIS A 481 ASN A 485 HIS A 495 ASN B 61 ASN B 104 HIS C 42 ASN C 53 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 HIS D 225 HIS D 353 GLN D 388 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 GLN D 455 ASN D 481 ASN D 495 ASN E 104 HIS F 42 ASN F 53 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 288 ASN G 373 GLN G 430 ASN G 455 ASN G 481 ASN ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS I 42 ASN I 53 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6052 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 17037 Z= 0.294 Angle : 0.829 9.475 23079 Z= 0.436 Chirality : 0.050 0.210 2547 Planarity : 0.007 0.075 2994 Dihedral : 7.629 71.183 2489 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.78 % Allowed : 12.01 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.16), residues: 2103 helix: -1.44 (0.27), residues: 312 sheet: -2.08 (0.21), residues: 552 loop : -2.70 (0.15), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 143 HIS 0.009 0.002 HIS G 275 PHE 0.029 0.003 PHE G 137 TYR 0.022 0.002 TYR D 488 ARG 0.011 0.001 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 275 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7312 (p0) cc_final: 0.6730 (t0) REVERT: A 141 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7229 (mmt) REVERT: A 170 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6668 (mp) REVERT: C 4 MET cc_start: 0.6320 (mmm) cc_final: 0.6100 (mmm) REVERT: D 174 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6033 (mm) REVERT: D 412 ASP cc_start: 0.6561 (t70) cc_final: 0.6306 (t0) REVERT: D 454 GLU cc_start: 0.6383 (tm-30) cc_final: 0.6127 (tm-30) REVERT: D 493 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5655 (mtt) REVERT: E 1 MET cc_start: 0.1395 (tmt) cc_final: -0.0165 (mtt) REVERT: E 49 MET cc_start: 0.6392 (mmm) cc_final: 0.5740 (mmm) REVERT: F 4 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6396 (tpp) REVERT: G 62 THR cc_start: 0.6887 (OUTLIER) cc_final: 0.6643 (p) REVERT: G 87 VAL cc_start: 0.7916 (m) cc_final: 0.7686 (p) REVERT: G 111 LYS cc_start: 0.7474 (mmtp) cc_final: 0.7254 (mppt) REVERT: G 252 LEU cc_start: 0.8118 (pp) cc_final: 0.7873 (mp) REVERT: G 274 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4651 (m-80) REVERT: G 386 ASN cc_start: 0.5742 (p0) cc_final: 0.5488 (p0) REVERT: G 463 CYS cc_start: 0.6923 (t) cc_final: 0.6552 (m) outliers start: 69 outliers final: 21 residues processed: 316 average time/residue: 1.0140 time to fit residues: 368.6197 Evaluate side-chains 200 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 420 TYR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 493 MET Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 274 TYR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 485 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN D 147 ASN D 155 GLN D 175 HIS D 368 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS E 40 GLN G 214 GLN G 264 GLN G 388 GLN ** G 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** G 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.7589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17037 Z= 0.310 Angle : 0.791 10.358 23079 Z= 0.409 Chirality : 0.049 0.225 2547 Planarity : 0.006 0.055 2994 Dihedral : 7.489 59.125 2487 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.17 % Allowed : 16.78 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2103 helix: -0.99 (0.28), residues: 318 sheet: -1.89 (0.20), residues: 618 loop : -2.38 (0.16), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 143 HIS 0.005 0.001 HIS G 8 PHE 0.031 0.003 PHE G 93 TYR 0.029 0.002 TYR D 420 ARG 0.011 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 200 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.4790 (mp0) REVERT: A 119 ASN cc_start: 0.7241 (p0) cc_final: 0.6588 (t0) REVERT: A 170 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.6759 (mp) REVERT: A 485 HIS cc_start: 0.7456 (p90) cc_final: 0.6838 (p-80) REVERT: B 37 TRP cc_start: 0.4564 (m100) cc_final: 0.4247 (m100) REVERT: D 174 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7091 (mm) REVERT: D 328 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6819 (tt) REVERT: D 365 LYS cc_start: 0.5437 (pttp) cc_final: 0.5172 (ptpt) REVERT: D 412 ASP cc_start: 0.6614 (t70) cc_final: 0.6251 (t0) REVERT: F 49 TYR cc_start: 0.5320 (p90) cc_final: 0.4968 (p90) REVERT: G 201 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: G 214 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6304 (mt0) REVERT: G 252 LEU cc_start: 0.8630 (pp) cc_final: 0.8248 (mt) REVERT: G 387 GLN cc_start: 0.6851 (tp-100) cc_final: 0.6057 (mm-40) REVERT: G 388 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6687 (pp30) REVERT: G 441 MET cc_start: 0.5241 (tpt) cc_final: 0.5006 (tpt) REVERT: G 442 ASP cc_start: 0.7516 (p0) cc_final: 0.7263 (p0) REVERT: G 444 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5994 (tp) REVERT: G 463 CYS cc_start: 0.8063 (t) cc_final: 0.7769 (m) REVERT: G 486 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6581 (tpm170) REVERT: I 33 LEU cc_start: 0.5765 (mp) cc_final: 0.5287 (mp) outliers start: 76 outliers final: 26 residues processed: 264 average time/residue: 1.0169 time to fit residues: 308.8229 Evaluate side-chains 187 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 303 GLN Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 214 GLN Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 388 GLN Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 444 LEU Chi-restraints excluded: chain G residue 495 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN G 288 ASN G 388 GLN G 430 ASN G 495 ASN I 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.8397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17037 Z= 0.228 Angle : 0.695 10.536 23079 Z= 0.358 Chirality : 0.046 0.205 2547 Planarity : 0.005 0.051 2994 Dihedral : 7.000 59.388 2487 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.00 % Allowed : 17.65 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.17), residues: 2103 helix: -0.56 (0.29), residues: 318 sheet: -1.64 (0.20), residues: 627 loop : -2.17 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 340 HIS 0.004 0.001 HIS G 8 PHE 0.026 0.002 PHE G 93 TYR 0.018 0.002 TYR D 488 ARG 0.005 0.001 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 178 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4674 (mp0) REVERT: A 119 ASN cc_start: 0.7204 (p0) cc_final: 0.6604 (t0) REVERT: A 170 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6739 (mp) REVERT: A 299 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5068 (mpp-170) REVERT: C 21 ILE cc_start: 0.6455 (tp) cc_final: 0.6172 (tt) REVERT: D 95 ASN cc_start: 0.8182 (t0) cc_final: 0.7938 (t0) REVERT: D 114 MET cc_start: 0.7768 (ttm) cc_final: 0.7232 (ttm) REVERT: D 174 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.7038 (mm) REVERT: D 328 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6898 (tt) REVERT: D 463 CYS cc_start: 0.7601 (m) cc_final: 0.6914 (t) REVERT: E 1 MET cc_start: 0.3891 (tmm) cc_final: 0.3617 (tmt) REVERT: E 49 MET cc_start: 0.5393 (mmm) cc_final: 0.5148 (mmm) REVERT: F 49 TYR cc_start: 0.5027 (p90) cc_final: 0.4672 (p90) REVERT: G 119 ASN cc_start: 0.6451 (p0) cc_final: 0.5577 (p0) REVERT: G 436 LEU cc_start: 0.7103 (mp) cc_final: 0.6469 (mt) REVERT: G 440 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6260 (mt-10) REVERT: G 453 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7390 (mtp-110) REVERT: G 454 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7113 (tm-30) REVERT: G 463 CYS cc_start: 0.7847 (t) cc_final: 0.7605 (m) REVERT: G 486 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6878 (tpm170) REVERT: I 89 GLN cc_start: 0.5534 (OUTLIER) cc_final: 0.5248 (pp30) outliers start: 73 outliers final: 33 residues processed: 238 average time/residue: 0.9399 time to fit residues: 259.2084 Evaluate side-chains 192 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain G residue 495 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN D 275 HIS D 314 ASN D 485 HIS G 451 GLN I 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.9262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17037 Z= 0.301 Angle : 0.744 10.887 23079 Z= 0.383 Chirality : 0.048 0.204 2547 Planarity : 0.005 0.056 2994 Dihedral : 7.317 68.673 2487 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 4.82 % Allowed : 18.75 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.18), residues: 2103 helix: -0.46 (0.30), residues: 318 sheet: -1.52 (0.21), residues: 597 loop : -2.07 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 143 HIS 0.009 0.002 HIS A 485 PHE 0.021 0.003 PHE E 79 TYR 0.028 0.002 TYR D 445 ARG 0.005 0.001 ARG D 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 162 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.4963 (mp0) REVERT: A 119 ASN cc_start: 0.7155 (p0) cc_final: 0.6680 (t0) REVERT: A 299 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6275 (mpp-170) REVERT: C 21 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6590 (tt) REVERT: D 22 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5533 (mp0) REVERT: D 95 ASN cc_start: 0.8097 (t0) cc_final: 0.7783 (t0) REVERT: D 114 MET cc_start: 0.7913 (ttm) cc_final: 0.7459 (ttm) REVERT: D 174 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7216 (mm) REVERT: D 255 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6601 (ptmm) REVERT: D 328 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6939 (tt) REVERT: D 463 CYS cc_start: 0.7628 (m) cc_final: 0.7010 (t) REVERT: G 119 ASN cc_start: 0.6912 (p0) cc_final: 0.5847 (t0) REVERT: G 145 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7377 (tt) REVERT: G 440 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6178 (mt-10) REVERT: G 453 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7159 (mtp-110) REVERT: G 454 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7365 (tm-30) REVERT: G 463 CYS cc_start: 0.7934 (t) cc_final: 0.7621 (m) REVERT: I 21 ILE cc_start: 0.7082 (mt) cc_final: 0.6663 (tp) REVERT: I 50 LYS cc_start: 0.6322 (tptp) cc_final: 0.6089 (mmmt) outliers start: 88 outliers final: 40 residues processed: 237 average time/residue: 0.9808 time to fit residues: 268.1428 Evaluate side-chains 191 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 388 GLN Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 166 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN I 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.9525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17037 Z= 0.225 Angle : 0.677 9.144 23079 Z= 0.350 Chirality : 0.047 0.228 2547 Planarity : 0.005 0.048 2994 Dihedral : 6.979 59.904 2487 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.44 % Allowed : 19.90 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 2103 helix: -0.24 (0.30), residues: 318 sheet: -1.27 (0.21), residues: 621 loop : -1.98 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 37 HIS 0.015 0.001 HIS A 485 PHE 0.016 0.002 PHE E 79 TYR 0.024 0.002 TYR D 445 ARG 0.008 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.4701 (mp0) REVERT: A 119 ASN cc_start: 0.7112 (p0) cc_final: 0.6665 (t0) REVERT: A 170 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.6686 (mp) REVERT: A 299 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5172 (mpp-170) REVERT: C 21 ILE cc_start: 0.6855 (tp) cc_final: 0.6597 (tt) REVERT: D 22 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5540 (mp0) REVERT: D 95 ASN cc_start: 0.8027 (t0) cc_final: 0.7750 (t0) REVERT: D 114 MET cc_start: 0.7818 (ttm) cc_final: 0.7338 (ttm) REVERT: D 119 ASN cc_start: 0.6932 (p0) cc_final: 0.6504 (t0) REVERT: D 255 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6815 (ptmm) REVERT: D 463 CYS cc_start: 0.7633 (m) cc_final: 0.7088 (t) REVERT: G 22 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.5207 (mp0) REVERT: G 69 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6709 (tm130) REVERT: G 119 ASN cc_start: 0.6790 (p0) cc_final: 0.6000 (t0) REVERT: G 145 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7451 (tt) REVERT: G 365 LYS cc_start: 0.6796 (OUTLIER) cc_final: 0.6393 (pttt) REVERT: G 440 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6201 (mt-10) REVERT: G 453 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7218 (mtp-110) REVERT: G 454 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7652 (tm-30) REVERT: G 463 CYS cc_start: 0.7851 (t) cc_final: 0.7543 (m) REVERT: I 21 ILE cc_start: 0.7081 (mt) cc_final: 0.6710 (tp) REVERT: I 38 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6635 (mp) REVERT: I 50 LYS cc_start: 0.6076 (tptp) cc_final: 0.5772 (mmmt) outliers start: 81 outliers final: 33 residues processed: 221 average time/residue: 0.9223 time to fit residues: 238.0191 Evaluate side-chains 192 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 168 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 199 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.9806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17037 Z= 0.195 Angle : 0.665 11.056 23079 Z= 0.340 Chirality : 0.045 0.222 2547 Planarity : 0.004 0.045 2994 Dihedral : 6.670 57.789 2487 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.40 % Allowed : 21.38 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.18), residues: 2103 helix: -0.03 (0.30), residues: 318 sheet: -1.15 (0.21), residues: 627 loop : -1.93 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 409 HIS 0.017 0.001 HIS A 485 PHE 0.017 0.002 PHE E 79 TYR 0.022 0.001 TYR D 445 ARG 0.007 0.000 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5434 (OUTLIER) cc_final: 0.4608 (mp0) REVERT: A 119 ASN cc_start: 0.7271 (p0) cc_final: 0.6867 (t0) REVERT: A 141 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7075 (mmt) REVERT: A 170 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6662 (mp) REVERT: A 299 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5095 (mpp-170) REVERT: C 21 ILE cc_start: 0.6946 (tp) cc_final: 0.6666 (tt) REVERT: D 22 GLU cc_start: 0.5803 (OUTLIER) cc_final: 0.5473 (mp0) REVERT: D 95 ASN cc_start: 0.8017 (t0) cc_final: 0.7734 (t0) REVERT: D 114 MET cc_start: 0.7800 (ttm) cc_final: 0.7389 (ttm) REVERT: D 119 ASN cc_start: 0.6905 (p0) cc_final: 0.6619 (t0) REVERT: D 255 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6705 (ptmm) REVERT: D 328 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6452 (tt) REVERT: D 463 CYS cc_start: 0.7418 (m) cc_final: 0.6970 (t) REVERT: D 485 HIS cc_start: 0.6765 (p-80) cc_final: 0.6505 (p90) REVERT: E 67 ARG cc_start: 0.6957 (ptp-110) cc_final: 0.6573 (ttt180) REVERT: G 69 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6665 (tm130) REVERT: G 119 ASN cc_start: 0.7058 (p0) cc_final: 0.6442 (t0) REVERT: G 145 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7412 (tt) REVERT: G 201 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6899 (t80) REVERT: G 365 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.6377 (pttt) REVERT: G 436 LEU cc_start: 0.7124 (mp) cc_final: 0.6871 (mt) REVERT: G 440 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6163 (mt-10) REVERT: G 453 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7086 (mtp-110) REVERT: G 463 CYS cc_start: 0.7752 (t) cc_final: 0.7500 (m) REVERT: I 4 MET cc_start: 0.6498 (mmm) cc_final: 0.6017 (mtm) REVERT: I 21 ILE cc_start: 0.7045 (mt) cc_final: 0.6748 (tp) REVERT: I 38 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6645 (mp) REVERT: I 50 LYS cc_start: 0.5887 (tptp) cc_final: 0.5632 (mmmt) outliers start: 62 outliers final: 29 residues processed: 211 average time/residue: 0.9407 time to fit residues: 230.4007 Evaluate side-chains 190 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.0060 chunk 126 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.9985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17037 Z= 0.300 Angle : 0.732 13.972 23079 Z= 0.375 Chirality : 0.048 0.311 2547 Planarity : 0.005 0.070 2994 Dihedral : 7.146 63.943 2487 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.06 % Allowed : 21.77 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2103 helix: -0.30 (0.30), residues: 318 sheet: -1.20 (0.21), residues: 633 loop : -1.95 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 409 HIS 0.016 0.001 HIS A 485 PHE 0.017 0.002 PHE E 79 TYR 0.033 0.002 TYR D 445 ARG 0.020 0.001 ARG G 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 151 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.4840 (mp0) REVERT: A 45 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7500 (ttmt) REVERT: A 119 ASN cc_start: 0.7144 (p0) cc_final: 0.6897 (t0) REVERT: A 201 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6111 (t80) REVERT: A 299 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5664 (mpp-170) REVERT: C 21 ILE cc_start: 0.7325 (tp) cc_final: 0.7060 (tt) REVERT: D 114 MET cc_start: 0.7872 (ttm) cc_final: 0.7458 (ttm) REVERT: D 203 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6920 (mp10) REVERT: D 255 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6729 (ptmm) REVERT: D 328 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6799 (tt) REVERT: D 387 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6985 (mm-40) REVERT: D 463 CYS cc_start: 0.7483 (m) cc_final: 0.7064 (t) REVERT: E 67 ARG cc_start: 0.7125 (ptp-110) cc_final: 0.6734 (ttt180) REVERT: F 21 ILE cc_start: 0.6845 (mt) cc_final: 0.6394 (tp) REVERT: G 69 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6667 (tm130) REVERT: G 119 ASN cc_start: 0.7050 (p0) cc_final: 0.6586 (t0) REVERT: G 145 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7385 (tt) REVERT: G 201 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6951 (t80) REVERT: G 395 GLU cc_start: 0.7357 (tt0) cc_final: 0.7058 (tt0) REVERT: G 436 LEU cc_start: 0.7243 (mp) cc_final: 0.6915 (mt) REVERT: G 440 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6214 (mt-10) REVERT: G 453 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7160 (mtp-110) REVERT: G 463 CYS cc_start: 0.7869 (t) cc_final: 0.7542 (m) REVERT: G 493 MET cc_start: 0.7356 (tpp) cc_final: 0.6132 (ttt) REVERT: I 4 MET cc_start: 0.6618 (mmm) cc_final: 0.6179 (mtm) REVERT: I 21 ILE cc_start: 0.7242 (mt) cc_final: 0.6901 (tp) REVERT: I 50 LYS cc_start: 0.5926 (tptp) cc_final: 0.5658 (mmmt) outliers start: 74 outliers final: 37 residues processed: 213 average time/residue: 1.0290 time to fit residues: 251.5201 Evaluate side-chains 194 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 145 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 1.0190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17037 Z= 0.213 Angle : 0.692 12.628 23079 Z= 0.350 Chirality : 0.046 0.278 2547 Planarity : 0.004 0.045 2994 Dihedral : 6.773 61.433 2487 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.12 % Allowed : 22.81 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 2103 helix: -0.15 (0.30), residues: 318 sheet: -1.16 (0.21), residues: 633 loop : -1.90 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 37 HIS 0.019 0.001 HIS A 485 PHE 0.016 0.002 PHE E 79 TYR 0.025 0.002 TYR D 445 ARG 0.005 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.4713 (mp0) REVERT: A 45 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7586 (ttpp) REVERT: A 119 ASN cc_start: 0.7174 (p0) cc_final: 0.6890 (t0) REVERT: A 159 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8015 (t) REVERT: A 170 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6669 (mp) REVERT: A 201 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6025 (t80) REVERT: A 299 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5094 (mpp-170) REVERT: B 67 ARG cc_start: 0.6206 (ptp-110) cc_final: 0.5778 (ttt180) REVERT: C 21 ILE cc_start: 0.7329 (tp) cc_final: 0.7043 (tt) REVERT: D 114 MET cc_start: 0.7840 (ttm) cc_final: 0.7437 (ttm) REVERT: D 119 ASN cc_start: 0.6847 (p0) cc_final: 0.6619 (t0) REVERT: D 255 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6769 (ptmm) REVERT: D 328 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6689 (tt) REVERT: D 353 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6886 (mp10) REVERT: D 463 CYS cc_start: 0.7454 (m) cc_final: 0.7005 (t) REVERT: E 67 ARG cc_start: 0.7135 (ptp-110) cc_final: 0.6715 (ttt180) REVERT: G 69 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6568 (tm130) REVERT: G 119 ASN cc_start: 0.7147 (p0) cc_final: 0.6723 (t0) REVERT: G 145 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7379 (tt) REVERT: G 201 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6848 (t80) REVERT: G 395 GLU cc_start: 0.7274 (tt0) cc_final: 0.6969 (tt0) REVERT: G 436 LEU cc_start: 0.7062 (mp) cc_final: 0.6810 (mt) REVERT: G 440 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6179 (mt-10) REVERT: G 453 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7126 (mtp-110) REVERT: G 463 CYS cc_start: 0.7773 (t) cc_final: 0.7493 (m) REVERT: G 493 MET cc_start: 0.7231 (tpp) cc_final: 0.5967 (ttt) REVERT: H 54 TYR cc_start: 0.6348 (p90) cc_final: 0.6110 (p90) REVERT: I 5 ASN cc_start: 0.6516 (t0) cc_final: 0.6219 (p0) REVERT: I 21 ILE cc_start: 0.7273 (mt) cc_final: 0.6981 (tp) REVERT: I 38 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6185 (mp) outliers start: 57 outliers final: 32 residues processed: 208 average time/residue: 0.9586 time to fit residues: 232.5520 Evaluate side-chains 195 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 388 GLN Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 93 optimal weight: 0.5980 chunk 136 optimal weight: 0.0070 chunk 206 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 485 HIS H 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 1.0308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17037 Z= 0.180 Angle : 0.654 12.175 23079 Z= 0.330 Chirality : 0.045 0.204 2547 Planarity : 0.004 0.044 2994 Dihedral : 6.487 57.898 2487 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.85 % Allowed : 23.79 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 2103 helix: -0.03 (0.30), residues: 318 sheet: -1.02 (0.21), residues: 633 loop : -1.83 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 37 HIS 0.017 0.001 HIS A 485 PHE 0.020 0.002 PHE G 93 TYR 0.026 0.001 TYR D 445 ARG 0.006 0.000 ARG A 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.5418 (OUTLIER) cc_final: 0.4615 (mp0) REVERT: A 45 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7486 (ttpp) REVERT: A 119 ASN cc_start: 0.7165 (p0) cc_final: 0.6937 (t0) REVERT: A 141 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: A 159 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8062 (t) REVERT: A 170 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.6687 (mp) REVERT: A 299 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5030 (mpp-170) REVERT: B 67 ARG cc_start: 0.6113 (ptp-110) cc_final: 0.5774 (ttt180) REVERT: D 114 MET cc_start: 0.7806 (ttm) cc_final: 0.7410 (ttm) REVERT: D 131 ARG cc_start: 0.6505 (mtp85) cc_final: 0.5259 (pmt-80) REVERT: D 328 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6689 (tt) REVERT: D 463 CYS cc_start: 0.7400 (m) cc_final: 0.6939 (t) REVERT: E 67 ARG cc_start: 0.7139 (ptp-110) cc_final: 0.6697 (ttt180) REVERT: F 21 ILE cc_start: 0.6491 (mm) cc_final: 0.6200 (tt) REVERT: G 69 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6563 (tm130) REVERT: G 119 ASN cc_start: 0.7076 (p0) cc_final: 0.6765 (t0) REVERT: G 145 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7383 (tt) REVERT: G 159 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8141 (t) REVERT: G 201 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6890 (t80) REVERT: G 270 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6116 (tt0) REVERT: G 436 LEU cc_start: 0.6978 (mp) cc_final: 0.6727 (mt) REVERT: G 440 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6161 (mt-10) REVERT: G 453 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7078 (mtp-110) REVERT: G 457 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5624 (mp0) REVERT: G 493 MET cc_start: 0.7047 (tpp) cc_final: 0.5837 (ttt) REVERT: I 5 ASN cc_start: 0.6525 (t0) cc_final: 0.6188 (p0) REVERT: I 21 ILE cc_start: 0.7175 (mt) cc_final: 0.6868 (tt) outliers start: 52 outliers final: 30 residues processed: 203 average time/residue: 0.9511 time to fit residues: 224.2356 Evaluate side-chains 192 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain C residue 23 CYS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 273 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain G residue 201 TYR Chi-restraints excluded: chain G residue 228 ILE Chi-restraints excluded: chain G residue 401 LYS Chi-restraints excluded: chain G residue 429 GLU Chi-restraints excluded: chain G residue 440 GLU Chi-restraints excluded: chain G residue 446 GLU Chi-restraints excluded: chain G residue 453 ARG Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.0770 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** A 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN D 240 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 394 ASN H 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.173380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.134501 restraints weight = 27043.844| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.14 r_work: 0.4046 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 1.0454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17037 Z= 0.173 Angle : 0.658 12.315 23079 Z= 0.331 Chirality : 0.044 0.205 2547 Planarity : 0.004 0.044 2994 Dihedral : 6.326 56.231 2487 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.69 % Allowed : 24.12 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.18), residues: 2103 helix: 0.01 (0.29), residues: 318 sheet: -0.89 (0.21), residues: 633 loop : -1.78 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 37 HIS 0.016 0.001 HIS A 485 PHE 0.017 0.001 PHE E 79 TYR 0.023 0.001 TYR D 445 ARG 0.010 0.000 ARG G 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5586.96 seconds wall clock time: 101 minutes 33.76 seconds (6093.76 seconds total)