Starting phenix.real_space_refine on Sat Aug 10 11:40:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w12_43714/08_2024/8w12_43714.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w12_43714/08_2024/8w12_43714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w12_43714/08_2024/8w12_43714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w12_43714/08_2024/8w12_43714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w12_43714/08_2024/8w12_43714.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w12_43714/08_2024/8w12_43714.cif" } resolution = 3.5 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= 0.008 sd= 0.071 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 166 5.16 5 C 18652 2.51 5 N 5070 2.21 5 O 5360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 157": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "D GLU 157": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D ASP 565": "OD1" <-> "OD2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 769": "OD1" <-> "OD2" Residue "D GLU 820": "OE1" <-> "OE2" Residue "D ASP 837": "OD1" <-> "OD2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E GLU 301": "OE1" <-> "OE2" Residue "E TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 684": "OE1" <-> "OE2" Residue "E GLU 724": "OE1" <-> "OE2" Residue "E TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 747": "OE1" <-> "OE2" Residue "E GLU 859": "OE1" <-> "OE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29248 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6889 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 44, 'TRANS': 807} Chain breaks: 3 Chain: "B" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6956 Classifications: {'peptide': 862} Link IDs: {'PTRANS': 43, 'TRANS': 818} Chain breaks: 2 Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "D" Number of atoms: 6889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6889 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 44, 'TRANS': 807} Chain breaks: 3 Chain: "E" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 862, 6956 Classifications: {'peptide': 862} Link IDs: {'PTRANS': 43, 'TRANS': 818} Chain breaks: 2 Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Time building chain proxies: 14.96, per 1000 atoms: 0.51 Number of scatterers: 29248 At special positions: 0 Unit cell: (204.6, 168.3, 143, 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 166 16.00 O 5360 8.00 N 5070 7.00 C 18652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.28 Conformation dependent library (CDL) restraints added in 5.0 seconds 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6908 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 51 sheets defined 48.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.580A pdb=" N ILE A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 4.005A pdb=" N GLN A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 removed outlier: 3.656A pdb=" N GLY A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 210 through 228 removed outlier: 3.820A pdb=" N GLN A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.608A pdb=" N ASN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.911A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.761A pdb=" N SER A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.626A pdb=" N ALA A 325 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.789A pdb=" N ARG A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 408 removed outlier: 3.612A pdb=" N ALA A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 509 through 537 Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 545 through 559 removed outlier: 4.735A pdb=" N LEU A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Proline residue: A 554 - end of helix Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.744A pdb=" N LEU A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 3.759A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.900A pdb=" N PHE A 636 " --> pdb=" O ARG A 632 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.659A pdb=" N LYS A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.677A pdb=" N LEU A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 691 Processing helix chain 'A' and resid 692 through 693 No H-bonds generated for 'chain 'A' and resid 692 through 693' Processing helix chain 'A' and resid 694 through 697 Processing helix chain 'A' and resid 717 through 724 removed outlier: 3.501A pdb=" N PHE A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 756 Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.598A pdb=" N ASP A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 3.540A pdb=" N LEU A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 835 removed outlier: 3.905A pdb=" N ASN A 834 " --> pdb=" O GLU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 868 removed outlier: 4.303A pdb=" N LEU A 867 " --> pdb=" O GLY A 864 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 868 " --> pdb=" O GLN A 865 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 864 through 868' Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'B' and resid 30 through 49 removed outlier: 4.508A pdb=" N ASP B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 76 removed outlier: 3.740A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 4.099A pdb=" N GLY B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 142 removed outlier: 3.667A pdb=" N PHE B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.742A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 removed outlier: 3.520A pdb=" N LEU B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 275 through 280 removed outlier: 3.507A pdb=" N TRP B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 297 Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 333 through 349 removed outlier: 3.792A pdb=" N PHE B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.997A pdb=" N ARG B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 407 Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 509 through 537 Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 545 through 559 removed outlier: 4.528A pdb=" N LEU B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Proline residue: B 554 - end of helix Processing helix chain 'B' and resid 573 through 581 removed outlier: 4.297A pdb=" N TRP B 577 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 removed outlier: 3.597A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.662A pdb=" N ASP B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 659 removed outlier: 3.523A pdb=" N LYS B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 672 Processing helix chain 'B' and resid 678 through 691 Processing helix chain 'B' and resid 694 through 697 Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 745 through 756 Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.839A pdb=" N ASP B 768 " --> pdb=" O ARG B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 removed outlier: 3.595A pdb=" N LEU B 795 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 839 Proline residue: B 836 - end of helix Processing helix chain 'B' and resid 864 through 866 No H-bonds generated for 'chain 'B' and resid 864 through 866' Processing helix chain 'B' and resid 885 through 893 removed outlier: 3.596A pdb=" N GLY B 893 " --> pdb=" O SER B 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 16 Processing helix chain 'C' and resid 16 through 23 removed outlier: 3.556A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.601A pdb=" N VAL C 279 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL C 280 " --> pdb=" O LYS C 277 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 281 " --> pdb=" O ASP C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 281' Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.789A pdb=" N VAL C 298 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 removed outlier: 4.351A pdb=" N GLU C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 48 Processing helix chain 'D' and resid 63 through 77 removed outlier: 3.542A pdb=" N ILE D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.592A pdb=" N SER D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 141 removed outlier: 3.502A pdb=" N GLY D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 210 through 228 removed outlier: 3.709A pdb=" N GLN D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 3.509A pdb=" N ASN D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 274 through 280 removed outlier: 4.478A pdb=" N VAL D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.815A pdb=" N SER D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 326 removed outlier: 3.621A pdb=" N ALA D 325 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D 326 " --> pdb=" O PRO D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 322 through 326' Processing helix chain 'D' and resid 333 through 349 removed outlier: 3.774A pdb=" N PHE D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.790A pdb=" N ARG D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 409 removed outlier: 3.571A pdb=" N ALA D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET D 409 " --> pdb=" O TYR D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 440 Processing helix chain 'D' and resid 494 through 507 Processing helix chain 'D' and resid 509 through 537 Proline residue: D 521 - end of helix Processing helix chain 'D' and resid 545 through 559 removed outlier: 4.564A pdb=" N LEU D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) Proline residue: D 554 - end of helix Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.987A pdb=" N TRP D 577 " --> pdb=" O TRP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 624 removed outlier: 3.779A pdb=" N ILE D 599 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 643 removed outlier: 3.920A pdb=" N PHE D 636 " --> pdb=" O ARG D 632 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 653 Processing helix chain 'D' and resid 663 through 672 removed outlier: 4.177A pdb=" N MET D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 672 " --> pdb=" O ARG D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 691 Processing helix chain 'D' and resid 717 through 724 Processing helix chain 'D' and resid 745 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 791 through 796 Processing helix chain 'D' and resid 830 through 839 removed outlier: 4.115A pdb=" N ASN D 834 " --> pdb=" O GLU D 831 " (cutoff:3.500A) Proline residue: D 836 - end of helix Processing helix chain 'D' and resid 885 through 890 Processing helix chain 'E' and resid 30 through 49 removed outlier: 4.407A pdb=" N ASP E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.773A pdb=" N ALA E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 removed outlier: 4.117A pdb=" N GLN E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 141 removed outlier: 3.690A pdb=" N PHE E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 176 through 188 Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.518A pdb=" N TYR E 214 " --> pdb=" O SER E 210 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 246 Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.924A pdb=" N PHE E 258 " --> pdb=" O VAL E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 284 through 297 removed outlier: 3.506A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 318 removed outlier: 3.895A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 333 through 349 removed outlier: 3.611A pdb=" N PHE E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 removed outlier: 4.059A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 379 " --> pdb=" O VAL E 375 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 407 removed outlier: 3.525A pdb=" N LEU E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 3.754A pdb=" N VAL E 438 " --> pdb=" O ASP E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 508 Processing helix chain 'E' and resid 510 through 538 Proline residue: E 521 - end of helix removed outlier: 3.730A pdb=" N LEU E 538 " --> pdb=" O ILE E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 559 removed outlier: 4.556A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Proline residue: E 554 - end of helix Processing helix chain 'E' and resid 574 through 582 Processing helix chain 'E' and resid 595 through 624 Processing helix chain 'E' and resid 632 through 643 removed outlier: 3.628A pdb=" N ASP E 643 " --> pdb=" O ALA E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 659 Processing helix chain 'E' and resid 662 through 671 Processing helix chain 'E' and resid 678 through 691 Processing helix chain 'E' and resid 717 through 724 Processing helix chain 'E' and resid 745 through 756 Processing helix chain 'E' and resid 757 through 768 removed outlier: 3.761A pdb=" N ASP E 768 " --> pdb=" O ARG E 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 796 removed outlier: 3.747A pdb=" N LEU E 795 " --> pdb=" O PRO E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 839 Proline residue: E 836 - end of helix Processing helix chain 'E' and resid 864 through 870 removed outlier: 5.418A pdb=" N LEU E 867 " --> pdb=" O GLY E 864 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL E 869 " --> pdb=" O ILE E 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 886 through 892 Processing helix chain 'F' and resid 9 through 23 removed outlier: 3.629A pdb=" N ILE F 13 " --> pdb=" O PRO F 9 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 15 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.547A pdb=" N VAL F 279 " --> pdb=" O ILE F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.755A pdb=" N VAL F 298 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS F 305 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 7.082A pdb=" N THR A 299 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 357 Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418 Processing sheet with id=AA9, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.209A pdb=" N THR A 780 " --> pdb=" O THR A 821 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 823 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG A 782 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR A 825 " --> pdb=" O ARG A 782 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS A 784 " --> pdb=" O TYR A 825 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 741 through 744 removed outlier: 6.680A pdb=" N VAL A 742 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 772 " --> pdb=" O MET A 705 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL A 703 " --> pdb=" O PHE A 774 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 848 " --> pdb=" O HIS A 706 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP A 708 " --> pdb=" O TYR A 846 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR A 846 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 800 through 804 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.542A pdb=" N VAL B 22 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 93 Processing sheet with id=AB6, first strand: chain 'B' and resid 150 through 153 Processing sheet with id=AB7, first strand: chain 'B' and resid 203 through 207 Processing sheet with id=AB8, first strand: chain 'B' and resid 299 through 303 removed outlier: 5.852A pdb=" N GLU B 301 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE B 303 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE B 584 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 353 through 357 Processing sheet with id=AC1, first strand: chain 'B' and resid 416 through 418 Processing sheet with id=AC2, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AC3, first strand: chain 'B' and resid 699 through 700 removed outlier: 3.638A pdb=" N THR B 700 " --> pdb=" O ARG B 779 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR B 780 " --> pdb=" O THR B 821 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE B 823 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG B 782 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR B 825 " --> pdb=" O ARG B 782 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS B 784 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 741 through 744 removed outlier: 3.616A pdb=" N VAL B 772 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL B 703 " --> pdb=" O PHE B 774 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 848 " --> pdb=" O HIS B 706 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 708 " --> pdb=" O TYR B 846 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR B 846 " --> pdb=" O ASP B 708 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 801 through 804 Processing sheet with id=AC6, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.627A pdb=" N GLN C 26 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET C 5 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N PHE C 286 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 7 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'D' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'D' and resid 90 through 94 Processing sheet with id=AD1, first strand: chain 'D' and resid 150 through 153 Processing sheet with id=AD2, first strand: chain 'D' and resid 193 through 197 Processing sheet with id=AD3, first strand: chain 'D' and resid 263 through 265 removed outlier: 3.565A pdb=" N MET D 884 " --> pdb=" O ILE D 264 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 353 through 357 Processing sheet with id=AD5, first strand: chain 'D' and resid 416 through 417 Processing sheet with id=AD6, first strand: chain 'D' and resid 457 through 458 Processing sheet with id=AD7, first strand: chain 'D' and resid 699 through 700 removed outlier: 3.550A pdb=" N THR D 700 " --> pdb=" O ARG D 779 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR D 780 " --> pdb=" O THR D 821 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE D 823 " --> pdb=" O THR D 780 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG D 782 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N TYR D 825 " --> pdb=" O ARG D 782 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LYS D 784 " --> pdb=" O TYR D 825 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 728 " --> pdb=" O LEU D 826 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 741 through 744 removed outlier: 6.643A pdb=" N VAL D 742 " --> pdb=" O ARG D 773 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL D 772 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE D 774 " --> pdb=" O VAL D 703 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL D 703 " --> pdb=" O PHE D 774 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 848 " --> pdb=" O HIS D 706 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP D 708 " --> pdb=" O TYR D 846 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR D 846 " --> pdb=" O ASP D 708 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 801 through 803 Processing sheet with id=AE1, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AE2, first strand: chain 'E' and resid 82 through 83 Processing sheet with id=AE3, first strand: chain 'E' and resid 166 through 167 removed outlier: 6.983A pdb=" N PHE E 90 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 150 through 152 Processing sheet with id=AE5, first strand: chain 'E' and resid 203 through 207 Processing sheet with id=AE6, first strand: chain 'E' and resid 264 through 266 removed outlier: 6.413A pdb=" N ILE E 264 " --> pdb=" O MET E 884 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 299 through 303 removed outlier: 7.108A pdb=" N THR E 299 " --> pdb=" O THR E 587 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 303 " --> pdb=" O SER E 583 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER E 583 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 353 through 357 removed outlier: 6.325A pdb=" N ILE E 354 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL E 571 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP E 356 " --> pdb=" O VAL E 571 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AF1, first strand: chain 'E' and resid 457 through 459 Processing sheet with id=AF2, first strand: chain 'E' and resid 699 through 700 removed outlier: 3.545A pdb=" N THR E 700 " --> pdb=" O ARG E 779 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 780 " --> pdb=" O THR E 821 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 823 " --> pdb=" O THR E 780 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG E 782 " --> pdb=" O ILE E 823 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR E 825 " --> pdb=" O ARG E 782 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS E 784 " --> pdb=" O TYR E 825 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE E 827 " --> pdb=" O LYS E 784 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR E 786 " --> pdb=" O ILE E 827 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 741 through 744 removed outlier: 3.576A pdb=" N VAL E 772 " --> pdb=" O MET E 705 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL E 703 " --> pdb=" O PHE E 774 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET E 848 " --> pdb=" O HIS E 706 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP E 708 " --> pdb=" O TYR E 846 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR E 846 " --> pdb=" O ASP E 708 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 801 through 804 Processing sheet with id=AF5, first strand: chain 'F' and resid 5 through 7 removed outlier: 6.203A pdb=" N LEU F 6 " --> pdb=" O SER F 273 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN F 26 " --> pdb=" O VAL F 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 284 through 287 1288 hydrogen bonds defined for protein. 3657 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: 10.57 Time building geometry restraints manager: 12.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9127 1.34 - 1.46: 5316 1.46 - 1.58: 15125 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 29880 Sorted by residual: bond pdb=" N THR E 421 " pdb=" CA THR E 421 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.37e-02 5.33e+03 7.73e+00 bond pdb=" C ALA F 260 " pdb=" N PRO F 261 " ideal model delta sigma weight residual 1.334 1.361 -0.027 1.11e-02 8.12e+03 6.09e+00 bond pdb=" N GLU A 160 " pdb=" CA GLU A 160 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.53e-02 4.27e+03 4.17e+00 bond pdb=" N GLY E 422 " pdb=" CA GLY E 422 " ideal model delta sigma weight residual 1.449 1.479 -0.029 1.45e-02 4.76e+03 4.11e+00 bond pdb=" CB PRO D 275 " pdb=" CG PRO D 275 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.59e+00 ... (remaining 29875 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.04: 660 105.04 - 112.32: 14592 112.32 - 119.61: 10447 119.61 - 126.89: 14484 126.89 - 134.18: 367 Bond angle restraints: 40550 Sorted by residual: angle pdb=" N PRO A 161 " pdb=" CA PRO A 161 " pdb=" C PRO A 161 " ideal model delta sigma weight residual 112.47 121.49 -9.02 2.06e+00 2.36e-01 1.92e+01 angle pdb=" CB LYS F 296 " pdb=" CG LYS F 296 " pdb=" CD LYS F 296 " ideal model delta sigma weight residual 111.30 120.93 -9.63 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CA LEU E 239 " pdb=" CB LEU E 239 " pdb=" CG LEU E 239 " ideal model delta sigma weight residual 116.30 129.68 -13.38 3.50e+00 8.16e-02 1.46e+01 angle pdb=" CB LYS C 296 " pdb=" CG LYS C 296 " pdb=" CD LYS C 296 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA THR E 421 " pdb=" C THR E 421 " pdb=" O THR E 421 " ideal model delta sigma weight residual 121.99 117.84 4.15 1.14e+00 7.69e-01 1.32e+01 ... (remaining 40545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 16191 17.94 - 35.89: 1592 35.89 - 53.83: 236 53.83 - 71.77: 46 71.77 - 89.72: 37 Dihedral angle restraints: 18102 sinusoidal: 7426 harmonic: 10676 Sorted by residual: dihedral pdb=" CA LEU A 379 " pdb=" C LEU A 379 " pdb=" N LEU A 380 " pdb=" CA LEU A 380 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN A 230 " pdb=" C GLN A 230 " pdb=" N GLU A 231 " pdb=" CA GLU A 231 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PRO B 645 " pdb=" C PRO B 645 " pdb=" N GLU B 646 " pdb=" CA GLU B 646 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 18099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3978 0.071 - 0.143: 543 0.143 - 0.214: 17 0.214 - 0.286: 3 0.286 - 0.357: 1 Chirality restraints: 4542 Sorted by residual: chirality pdb=" CB ILE D 326 " pdb=" CA ILE D 326 " pdb=" CG1 ILE D 326 " pdb=" CG2 ILE D 326 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CB THR A 835 " pdb=" CA THR A 835 " pdb=" OG1 THR A 835 " pdb=" CG2 THR A 835 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU E 239 " pdb=" CB LEU E 239 " pdb=" CD1 LEU E 239 " pdb=" CD2 LEU E 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4539 not shown) Planarity restraints: 5250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 331 " -0.065 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO D 332 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO D 332 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 332 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 637 " 0.014 2.00e-02 2.50e+03 1.33e-02 4.44e+00 pdb=" CG TRP A 637 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 637 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 637 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 637 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 637 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 637 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 637 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 637 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 637 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 502 " -0.164 9.50e-02 1.11e+02 7.38e-02 4.12e+00 pdb=" NE ARG E 502 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 502 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG E 502 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 502 " -0.001 2.00e-02 2.50e+03 ... (remaining 5247 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3427 2.76 - 3.29: 29022 3.29 - 3.83: 46718 3.83 - 4.36: 50314 4.36 - 4.90: 88616 Nonbonded interactions: 218097 Sorted by model distance: nonbonded pdb=" O PHE B 324 " pdb=" OG1 THR B 328 " model vdw 2.219 3.040 nonbonded pdb=" OG SER D 251 " pdb=" OE1 GLU D 253 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP B 885 " pdb=" OG1 THR B 887 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 812 " pdb=" OG SER E 838 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 838 " pdb=" OH TYR D 812 " model vdw 2.244 3.040 ... (remaining 218092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 49 or resid 63 through 480 or resid 489 through \ 892)) selection = (chain 'B' and (resid 24 through 655 or resid 662 through 806 or resid 811 throu \ gh 892)) selection = (chain 'D' and (resid 24 through 49 or resid 63 through 480 or resid 489 through \ 892)) selection = (chain 'E' and (resid 24 through 655 or resid 662 through 806 or resid 811 throu \ gh 892)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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 group one per residue 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: 0.680 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: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 73.410 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.130 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.003 0.080 29880 Z= 0.193 Angle : 0.701 13.380 40550 Z= 0.351 Chirality : 0.046 0.357 4542 Planarity : 0.005 0.098 5250 Dihedral : 14.489 89.716 11194 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3592 helix: 0.76 (0.13), residues: 1568 sheet: -0.33 (0.27), residues: 370 loop : -1.13 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 637 HIS 0.011 0.001 HIS B 244 PHE 0.029 0.001 PHE A 527 TYR 0.024 0.001 TYR E 746 ARG 0.016 0.001 ARG E 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 859 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.7490 (pp20) cc_final: 0.7242 (pp20) REVERT: A 111 MET cc_start: 0.8786 (tmm) cc_final: 0.8282 (tmm) REVERT: A 248 ILE cc_start: 0.8781 (tp) cc_final: 0.8567 (pt) REVERT: A 257 ASP cc_start: 0.7886 (m-30) cc_final: 0.7650 (m-30) REVERT: A 371 MET cc_start: 0.6593 (mtm) cc_final: 0.6368 (mtt) REVERT: A 381 PHE cc_start: 0.8731 (m-10) cc_final: 0.8487 (m-10) REVERT: A 439 PHE cc_start: 0.7656 (t80) cc_final: 0.7339 (t80) REVERT: A 501 LEU cc_start: 0.8556 (tp) cc_final: 0.8277 (tp) REVERT: A 552 LEU cc_start: 0.8581 (tt) cc_final: 0.8300 (tp) REVERT: A 636 PHE cc_start: 0.7689 (p90) cc_final: 0.7445 (p90) REVERT: A 685 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 709 MET cc_start: 0.8548 (pmm) cc_final: 0.8315 (pmm) REVERT: B 18 LEU cc_start: 0.8771 (tt) cc_final: 0.8453 (tt) REVERT: B 44 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7708 (ttm170) REVERT: B 113 GLN cc_start: 0.8447 (mm110) cc_final: 0.8244 (mp10) REVERT: B 339 ASP cc_start: 0.8097 (m-30) cc_final: 0.7785 (m-30) REVERT: B 433 GLN cc_start: 0.8252 (mp10) cc_final: 0.7993 (mp10) REVERT: B 503 MET cc_start: 0.8020 (tmm) cc_final: 0.7777 (tmm) REVERT: B 519 MET cc_start: 0.8743 (mmm) cc_final: 0.8424 (mmm) REVERT: B 643 ASP cc_start: 0.8168 (t0) cc_final: 0.7945 (t0) REVERT: B 652 MET cc_start: 0.9120 (tpp) cc_final: 0.8912 (mmp) REVERT: B 667 MET cc_start: 0.8010 (mmm) cc_final: 0.7159 (mmm) REVERT: B 731 MET cc_start: 0.8354 (tpp) cc_final: 0.8110 (tpp) REVERT: D 99 ASP cc_start: 0.8240 (p0) cc_final: 0.7850 (p0) REVERT: D 111 MET cc_start: 0.8557 (tpp) cc_final: 0.8222 (tpp) REVERT: D 161 PRO cc_start: 0.9144 (Cg_exo) cc_final: 0.8939 (Cg_endo) REVERT: D 169 LYS cc_start: 0.8401 (mmmm) cc_final: 0.7947 (mmmt) REVERT: D 209 CYS cc_start: 0.8078 (t) cc_final: 0.7842 (t) REVERT: D 253 GLU cc_start: 0.7722 (mp0) cc_final: 0.7473 (mp0) REVERT: D 257 ASP cc_start: 0.7850 (m-30) cc_final: 0.7501 (m-30) REVERT: D 536 GLU cc_start: 0.7876 (tp30) cc_final: 0.7646 (tp30) REVERT: D 620 MET cc_start: 0.8237 (tpp) cc_final: 0.7993 (tpp) REVERT: D 642 ASN cc_start: 0.8586 (m110) cc_final: 0.8311 (m110) REVERT: D 684 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7790 (tp30) REVERT: D 708 ASP cc_start: 0.8413 (p0) cc_final: 0.8196 (p0) REVERT: E 44 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7840 (ptm160) REVERT: E 70 ASP cc_start: 0.7691 (t70) cc_final: 0.7319 (t0) REVERT: E 111 MET cc_start: 0.9027 (tmm) cc_final: 0.8413 (tmm) REVERT: E 113 GLN cc_start: 0.8447 (mp10) cc_final: 0.8153 (mp10) REVERT: E 339 ASP cc_start: 0.8248 (m-30) cc_final: 0.7820 (m-30) REVERT: E 411 ASN cc_start: 0.8440 (t0) cc_final: 0.8189 (t0) REVERT: E 498 ASN cc_start: 0.8375 (t0) cc_final: 0.8150 (t0) REVERT: E 600 GLU cc_start: 0.7779 (pt0) cc_final: 0.7530 (pt0) REVERT: E 642 ASN cc_start: 0.8471 (t0) cc_final: 0.8242 (t0) REVERT: E 667 MET cc_start: 0.8056 (mmm) cc_final: 0.7092 (mmm) outliers start: 0 outliers final: 0 residues processed: 859 average time/residue: 0.4144 time to fit residues: 550.9326 Evaluate side-chains 770 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 770 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN D 531 ASN E 467 HIS ** E 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29880 Z= 0.273 Angle : 0.635 12.542 40550 Z= 0.324 Chirality : 0.044 0.203 4542 Planarity : 0.005 0.061 5250 Dihedral : 4.163 20.228 4040 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 11.92 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3592 helix: 1.27 (0.13), residues: 1564 sheet: -0.33 (0.27), residues: 380 loop : -0.96 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 637 HIS 0.013 0.001 HIS D 378 PHE 0.024 0.002 PHE E 694 TYR 0.023 0.002 TYR B 410 ARG 0.008 0.001 ARG E 502 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 778 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7981 (tptm) cc_final: 0.7621 (tptm) REVERT: A 110 GLU cc_start: 0.7561 (pp20) cc_final: 0.7253 (tm-30) REVERT: A 111 MET cc_start: 0.8928 (tmm) cc_final: 0.8299 (tmm) REVERT: A 160 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8155 (mm-30) REVERT: A 257 ASP cc_start: 0.8089 (m-30) cc_final: 0.7846 (m-30) REVERT: A 381 PHE cc_start: 0.8559 (m-10) cc_final: 0.8107 (m-80) REVERT: A 664 ARG cc_start: 0.7192 (ptt-90) cc_final: 0.6873 (ptt-90) REVERT: A 668 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: A 709 MET cc_start: 0.8546 (pmm) cc_final: 0.8322 (pmm) REVERT: A 831 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 36 LEU cc_start: 0.8950 (mm) cc_final: 0.8711 (mm) REVERT: B 44 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7651 (ttm170) REVERT: B 167 GLU cc_start: 0.8230 (pp20) cc_final: 0.7874 (pp20) REVERT: B 339 ASP cc_start: 0.8226 (m-30) cc_final: 0.7901 (m-30) REVERT: B 433 GLN cc_start: 0.8284 (mp10) cc_final: 0.8077 (mp-120) REVERT: B 512 GLU cc_start: 0.8144 (mp0) cc_final: 0.7943 (mp0) REVERT: B 643 ASP cc_start: 0.8262 (t0) cc_final: 0.8019 (t0) REVERT: B 666 MET cc_start: 0.8423 (tpp) cc_final: 0.8131 (tpt) REVERT: B 667 MET cc_start: 0.8076 (mmm) cc_final: 0.7556 (mmm) REVERT: B 685 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 686 GLU cc_start: 0.7848 (tp30) cc_final: 0.7579 (tp30) REVERT: B 724 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7868 (mm-30) REVERT: B 731 MET cc_start: 0.8478 (tpp) cc_final: 0.8182 (tpp) REVERT: D 44 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7463 (mtt180) REVERT: D 66 LYS cc_start: 0.8436 (tptm) cc_final: 0.8211 (tptm) REVERT: D 99 ASP cc_start: 0.8300 (p0) cc_final: 0.7894 (p0) REVERT: D 111 MET cc_start: 0.8672 (tpp) cc_final: 0.8299 (tpp) REVERT: D 201 ASP cc_start: 0.7602 (p0) cc_final: 0.7154 (p0) REVERT: D 209 CYS cc_start: 0.8046 (t) cc_final: 0.7813 (t) REVERT: D 253 GLU cc_start: 0.7943 (mp0) cc_final: 0.7620 (mp0) REVERT: D 257 ASP cc_start: 0.7884 (m-30) cc_final: 0.7580 (m-30) REVERT: D 342 LYS cc_start: 0.8551 (ptpp) cc_final: 0.8234 (ptpp) REVERT: D 344 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7745 (t80) REVERT: D 348 MET cc_start: 0.8168 (tpp) cc_final: 0.7672 (tpp) REVERT: D 610 MET cc_start: 0.8217 (mmm) cc_final: 0.7864 (mtt) REVERT: D 620 MET cc_start: 0.8307 (tpp) cc_final: 0.7990 (tpp) REVERT: D 684 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7985 (tp30) REVERT: D 712 GLU cc_start: 0.7505 (pm20) cc_final: 0.7054 (pm20) REVERT: E 36 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8543 (mm) REVERT: E 44 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7846 (ptm160) REVERT: E 81 LYS cc_start: 0.8013 (ptmm) cc_final: 0.7801 (ptmm) REVERT: E 111 MET cc_start: 0.9053 (tmm) cc_final: 0.8536 (tmm) REVERT: E 202 VAL cc_start: 0.8308 (t) cc_final: 0.8013 (m) REVERT: E 339 ASP cc_start: 0.8322 (m-30) cc_final: 0.7829 (m-30) REVERT: E 409 MET cc_start: 0.7861 (mmt) cc_final: 0.7438 (mmt) REVERT: E 467 HIS cc_start: 0.6638 (p90) cc_final: 0.6423 (p-80) REVERT: E 498 ASN cc_start: 0.8456 (t0) cc_final: 0.8222 (t0) REVERT: E 503 MET cc_start: 0.8365 (tpp) cc_final: 0.8138 (tpp) REVERT: E 524 MET cc_start: 0.8592 (mmm) cc_final: 0.8289 (mmm) REVERT: E 638 LYS cc_start: 0.8798 (tppt) cc_final: 0.8590 (tppt) REVERT: E 642 ASN cc_start: 0.8614 (t0) cc_final: 0.8378 (t0) REVERT: E 667 MET cc_start: 0.7998 (mmm) cc_final: 0.7592 (mmm) REVERT: E 698 MET cc_start: 0.9029 (mmt) cc_final: 0.8805 (mmt) REVERT: F 26 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6746 (mm-40) outliers start: 61 outliers final: 40 residues processed: 797 average time/residue: 0.4168 time to fit residues: 516.1038 Evaluate side-chains 800 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 758 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 182 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 273 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 355 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 264 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN ** A 723 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN D 642 ASN E 523 HIS E 539 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29880 Z= 0.343 Angle : 0.671 10.515 40550 Z= 0.345 Chirality : 0.046 0.206 4542 Planarity : 0.005 0.055 5250 Dihedral : 4.458 23.418 4040 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.36 % Allowed : 15.65 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.14), residues: 3592 helix: 1.19 (0.13), residues: 1596 sheet: -0.45 (0.26), residues: 382 loop : -1.08 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 637 HIS 0.012 0.001 HIS A 378 PHE 0.030 0.002 PHE D 324 TYR 0.024 0.002 TYR B 744 ARG 0.008 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 788 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8158 (tptm) cc_final: 0.7411 (tptm) REVERT: A 70 ASP cc_start: 0.7910 (m-30) cc_final: 0.7380 (m-30) REVERT: A 111 MET cc_start: 0.8933 (tmm) cc_final: 0.8200 (tmm) REVERT: A 169 LYS cc_start: 0.8903 (mppt) cc_final: 0.8675 (mppt) REVERT: A 253 GLU cc_start: 0.8335 (mp0) cc_final: 0.7886 (mp0) REVERT: A 257 ASP cc_start: 0.8189 (m-30) cc_final: 0.7963 (m-30) REVERT: A 381 PHE cc_start: 0.8435 (m-10) cc_final: 0.8151 (m-80) REVERT: A 501 LEU cc_start: 0.8643 (tp) cc_final: 0.8355 (tp) REVERT: A 578 PHE cc_start: 0.8237 (m-80) cc_final: 0.7532 (m-80) REVERT: A 637 TRP cc_start: 0.8377 (t60) cc_final: 0.7990 (t60) REVERT: A 641 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8118 (mt) REVERT: A 664 ARG cc_start: 0.7232 (ptt-90) cc_final: 0.6579 (ttp-110) REVERT: A 668 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8176 (mtm-85) REVERT: A 709 MET cc_start: 0.8586 (pmm) cc_final: 0.8341 (pmm) REVERT: A 712 GLU cc_start: 0.7619 (pm20) cc_final: 0.7159 (pm20) REVERT: B 36 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 44 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7743 (ttm170) REVERT: B 293 ILE cc_start: 0.9199 (tt) cc_final: 0.8938 (pt) REVERT: B 339 ASP cc_start: 0.8252 (m-30) cc_final: 0.8052 (m-30) REVERT: B 406 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8865 (mp) REVERT: B 454 THR cc_start: 0.8837 (p) cc_final: 0.8492 (p) REVERT: B 512 GLU cc_start: 0.8284 (mp0) cc_final: 0.7946 (mp0) REVERT: B 643 ASP cc_start: 0.8376 (t0) cc_final: 0.8142 (t0) REVERT: B 667 MET cc_start: 0.8137 (mmm) cc_final: 0.7710 (mmm) REVERT: B 685 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 724 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7981 (mm-30) REVERT: C 266 GLU cc_start: 0.6879 (tt0) cc_final: 0.6091 (mt-10) REVERT: C 314 THR cc_start: 0.6760 (t) cc_final: 0.6520 (t) REVERT: D 44 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7531 (mtt180) REVERT: D 66 LYS cc_start: 0.8413 (tptm) cc_final: 0.8034 (tptm) REVERT: D 99 ASP cc_start: 0.8265 (p0) cc_final: 0.7898 (p0) REVERT: D 111 MET cc_start: 0.8744 (tpp) cc_final: 0.8308 (tpp) REVERT: D 201 ASP cc_start: 0.7593 (p0) cc_final: 0.7132 (p0) REVERT: D 209 CYS cc_start: 0.8088 (t) cc_final: 0.7864 (t) REVERT: D 253 GLU cc_start: 0.7945 (mp0) cc_final: 0.7626 (mp0) REVERT: D 257 ASP cc_start: 0.8083 (m-30) cc_final: 0.7710 (m-30) REVERT: D 342 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8219 (ptpp) REVERT: D 344 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7543 (t80) REVERT: D 348 MET cc_start: 0.8210 (tpp) cc_final: 0.7734 (tpp) REVERT: D 519 MET cc_start: 0.7472 (mmp) cc_final: 0.6195 (mmt) REVERT: D 573 TRP cc_start: 0.8256 (m100) cc_final: 0.7988 (m100) REVERT: D 620 MET cc_start: 0.8403 (tpp) cc_final: 0.8076 (tpp) REVERT: D 642 ASN cc_start: 0.8815 (m-40) cc_final: 0.8227 (m110) REVERT: D 684 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7952 (tp30) REVERT: E 36 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8633 (mm) REVERT: E 44 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7877 (ptm160) REVERT: E 69 ASP cc_start: 0.7999 (m-30) cc_final: 0.7799 (m-30) REVERT: E 70 ASP cc_start: 0.8029 (t0) cc_final: 0.7481 (t0) REVERT: E 111 MET cc_start: 0.8941 (tmm) cc_final: 0.8127 (tmm) REVERT: E 202 VAL cc_start: 0.8302 (t) cc_final: 0.8063 (m) REVERT: E 339 ASP cc_start: 0.8344 (m-30) cc_final: 0.7857 (m-30) REVERT: E 409 MET cc_start: 0.7946 (mmt) cc_final: 0.7286 (mmt) REVERT: E 498 ASN cc_start: 0.8444 (t0) cc_final: 0.8193 (t0) REVERT: E 529 ARG cc_start: 0.7119 (ttt90) cc_final: 0.6773 (ttt90) REVERT: E 593 LEU cc_start: 0.8913 (tt) cc_final: 0.8708 (tp) REVERT: E 622 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7507 (tpp80) REVERT: E 638 LYS cc_start: 0.8832 (tppt) cc_final: 0.8613 (tppt) REVERT: E 642 ASN cc_start: 0.8708 (t0) cc_final: 0.8499 (t0) REVERT: E 848 MET cc_start: 0.8123 (mmt) cc_final: 0.7919 (mmt) REVERT: F 26 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6727 (mm-40) outliers start: 107 outliers final: 77 residues processed: 839 average time/residue: 0.4372 time to fit residues: 573.1597 Evaluate side-chains 846 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 764 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 403 ASN Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 325 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 170 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 330 optimal weight: 0.9980 chunk 349 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 313 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN E 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29880 Z= 0.176 Angle : 0.622 13.263 40550 Z= 0.312 Chirality : 0.043 0.219 4542 Planarity : 0.004 0.050 5250 Dihedral : 4.197 21.335 4040 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.85 % Allowed : 18.22 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3592 helix: 1.38 (0.13), residues: 1594 sheet: -0.37 (0.26), residues: 382 loop : -1.01 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 238 HIS 0.010 0.001 HIS B 378 PHE 0.026 0.001 PHE D 636 TYR 0.020 0.001 TYR E 17 ARG 0.006 0.000 ARG D 623 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 790 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.7888 (m-30) cc_final: 0.7575 (m-30) REVERT: A 111 MET cc_start: 0.8864 (tmm) cc_final: 0.8176 (tmm) REVERT: A 257 ASP cc_start: 0.8151 (m-30) cc_final: 0.7883 (m-30) REVERT: A 344 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.7981 (t80) REVERT: A 381 PHE cc_start: 0.8247 (m-10) cc_final: 0.7951 (m-10) REVERT: A 614 MET cc_start: 0.7699 (tpt) cc_final: 0.7489 (tpt) REVERT: A 637 TRP cc_start: 0.8370 (t60) cc_final: 0.8067 (t60) REVERT: A 664 ARG cc_start: 0.7120 (ptt-90) cc_final: 0.6743 (ttp-110) REVERT: A 709 MET cc_start: 0.8508 (pmm) cc_final: 0.8296 (pmm) REVERT: A 831 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 878 LYS cc_start: 0.7745 (mppt) cc_final: 0.7536 (mmtm) REVERT: B 339 ASP cc_start: 0.8166 (m-30) cc_final: 0.7817 (m-30) REVERT: B 345 LEU cc_start: 0.9243 (tp) cc_final: 0.9008 (tt) REVERT: B 355 LEU cc_start: 0.7919 (mm) cc_final: 0.7644 (mm) REVERT: B 406 LEU cc_start: 0.9041 (mm) cc_final: 0.8764 (mp) REVERT: B 512 GLU cc_start: 0.8227 (mp0) cc_final: 0.7904 (mp0) REVERT: B 643 ASP cc_start: 0.8331 (t0) cc_final: 0.8081 (t0) REVERT: B 667 MET cc_start: 0.7967 (mmm) cc_final: 0.7734 (mmm) REVERT: B 685 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 724 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7868 (mm-30) REVERT: B 869 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8634 (t) REVERT: C 314 THR cc_start: 0.6868 (t) cc_final: 0.6586 (t) REVERT: D 44 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7514 (mtt180) REVERT: D 66 LYS cc_start: 0.8398 (tptm) cc_final: 0.8058 (tptm) REVERT: D 99 ASP cc_start: 0.8191 (p0) cc_final: 0.7827 (p0) REVERT: D 109 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7905 (mm-30) REVERT: D 111 MET cc_start: 0.8787 (tpp) cc_final: 0.8458 (tpp) REVERT: D 169 LYS cc_start: 0.8401 (mmmm) cc_final: 0.7899 (mmmt) REVERT: D 209 CYS cc_start: 0.7870 (t) cc_final: 0.7597 (t) REVERT: D 253 GLU cc_start: 0.7926 (mp0) cc_final: 0.7567 (mp0) REVERT: D 257 ASP cc_start: 0.7996 (m-30) cc_final: 0.7628 (m-30) REVERT: D 342 LYS cc_start: 0.8522 (ptpp) cc_final: 0.8160 (ptpp) REVERT: D 344 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7605 (t80) REVERT: D 348 MET cc_start: 0.8095 (tpp) cc_final: 0.7591 (tpp) REVERT: D 394 MET cc_start: 0.8456 (ttm) cc_final: 0.8225 (mtm) REVERT: D 409 MET cc_start: 0.6948 (tpt) cc_final: 0.6679 (tpp) REVERT: D 519 MET cc_start: 0.7292 (mmp) cc_final: 0.6263 (mmp) REVERT: D 552 LEU cc_start: 0.8743 (tt) cc_final: 0.8434 (tp) REVERT: D 573 TRP cc_start: 0.8213 (m100) cc_final: 0.7915 (m100) REVERT: D 620 MET cc_start: 0.8347 (tpp) cc_final: 0.7977 (tpp) REVERT: D 642 ASN cc_start: 0.8832 (m-40) cc_final: 0.8047 (m-40) REVERT: E 36 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8510 (mm) REVERT: E 44 ARG cc_start: 0.8153 (ttp-170) cc_final: 0.7848 (ptm160) REVERT: E 111 MET cc_start: 0.8989 (tmm) cc_final: 0.8154 (tmm) REVERT: E 202 VAL cc_start: 0.8322 (t) cc_final: 0.8072 (m) REVERT: E 339 ASP cc_start: 0.8280 (m-30) cc_final: 0.7803 (m-30) REVERT: E 409 MET cc_start: 0.7953 (mmt) cc_final: 0.7242 (mmt) REVERT: E 411 ASN cc_start: 0.8361 (t0) cc_final: 0.8060 (t0) REVERT: E 498 ASN cc_start: 0.8415 (t0) cc_final: 0.8162 (t0) REVERT: E 529 ARG cc_start: 0.7091 (ttt90) cc_final: 0.6791 (ttt-90) REVERT: E 611 LYS cc_start: 0.8985 (tttp) cc_final: 0.8740 (tppt) REVERT: E 622 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7305 (tpp80) REVERT: E 642 ASN cc_start: 0.8696 (t0) cc_final: 0.8443 (t0) REVERT: E 667 MET cc_start: 0.8142 (mmm) cc_final: 0.7500 (mmm) REVERT: E 686 GLU cc_start: 0.7830 (tp30) cc_final: 0.7627 (tp30) REVERT: E 698 MET cc_start: 0.8917 (mmt) cc_final: 0.8618 (mmm) REVERT: E 848 MET cc_start: 0.8023 (mmt) cc_final: 0.7742 (mmt) REVERT: F 26 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6661 (mm-40) outliers start: 91 outliers final: 63 residues processed: 831 average time/residue: 0.3828 time to fit residues: 497.6026 Evaluate side-chains 826 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 759 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 291 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN B 796 GLN D 397 GLN E 539 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29880 Z= 0.330 Angle : 0.678 11.914 40550 Z= 0.346 Chirality : 0.045 0.204 4542 Planarity : 0.005 0.095 5250 Dihedral : 4.449 23.561 4040 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.14 % Allowed : 19.51 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3592 helix: 1.26 (0.13), residues: 1598 sheet: -0.51 (0.26), residues: 402 loop : -1.10 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 238 HIS 0.012 0.001 HIS D 378 PHE 0.034 0.002 PHE D 324 TYR 0.022 0.002 TYR E 17 ARG 0.015 0.001 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 784 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.7927 (m-30) cc_final: 0.7645 (m-30) REVERT: A 111 MET cc_start: 0.8770 (tmm) cc_final: 0.8167 (tmm) REVERT: A 253 GLU cc_start: 0.8299 (mp0) cc_final: 0.7849 (mp0) REVERT: A 257 ASP cc_start: 0.8231 (m-30) cc_final: 0.7993 (m-30) REVERT: A 381 PHE cc_start: 0.8366 (m-10) cc_final: 0.8099 (m-10) REVERT: A 481 GLU cc_start: 0.8234 (mp0) cc_final: 0.7847 (mp0) REVERT: A 501 LEU cc_start: 0.8661 (tp) cc_final: 0.8385 (tp) REVERT: A 578 PHE cc_start: 0.8180 (m-80) cc_final: 0.7506 (m-80) REVERT: A 582 ARG cc_start: 0.8169 (mmp80) cc_final: 0.7916 (mmp-170) REVERT: A 637 TRP cc_start: 0.8502 (t60) cc_final: 0.8063 (t60) REVERT: A 641 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.7985 (mt) REVERT: A 664 ARG cc_start: 0.7411 (ptt-90) cc_final: 0.6969 (ptt-90) REVERT: A 668 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8378 (mtm-85) REVERT: A 709 MET cc_start: 0.8579 (pmm) cc_final: 0.8309 (pmm) REVERT: B 17 TYR cc_start: 0.7738 (p90) cc_final: 0.7195 (p90) REVERT: B 36 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8749 (mm) REVERT: B 47 GLN cc_start: 0.8007 (pp30) cc_final: 0.7805 (tm-30) REVERT: B 95 MET cc_start: 0.7308 (pmm) cc_final: 0.7105 (pmm) REVERT: B 111 MET cc_start: 0.8635 (tpp) cc_final: 0.8356 (tpp) REVERT: B 291 MET cc_start: 0.8153 (tmm) cc_final: 0.7734 (tmm) REVERT: B 339 ASP cc_start: 0.8198 (m-30) cc_final: 0.7820 (m-30) REVERT: B 355 LEU cc_start: 0.8037 (mm) cc_final: 0.7760 (mm) REVERT: B 667 MET cc_start: 0.8144 (mmm) cc_final: 0.7925 (mmm) REVERT: B 724 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7869 (mm-30) REVERT: B 861 VAL cc_start: 0.8597 (m) cc_final: 0.8327 (t) REVERT: C 314 THR cc_start: 0.7102 (t) cc_final: 0.6893 (t) REVERT: D 44 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7615 (mtt180) REVERT: D 66 LYS cc_start: 0.8411 (tptm) cc_final: 0.8022 (tptm) REVERT: D 99 ASP cc_start: 0.8243 (p0) cc_final: 0.7934 (p0) REVERT: D 111 MET cc_start: 0.8795 (tpp) cc_final: 0.8354 (tpp) REVERT: D 209 CYS cc_start: 0.8036 (t) cc_final: 0.7797 (t) REVERT: D 253 GLU cc_start: 0.7938 (mp0) cc_final: 0.7332 (mp0) REVERT: D 257 ASP cc_start: 0.8112 (m-30) cc_final: 0.7749 (m-30) REVERT: D 342 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8219 (ptpp) REVERT: D 344 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.7584 (t80) REVERT: D 348 MET cc_start: 0.8135 (tpp) cc_final: 0.7615 (tpp) REVERT: D 449 TYR cc_start: 0.7980 (m-80) cc_final: 0.7731 (m-80) REVERT: D 573 TRP cc_start: 0.8291 (m100) cc_final: 0.7994 (m100) REVERT: E 36 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8646 (mm) REVERT: E 44 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7912 (ptm160) REVERT: E 111 MET cc_start: 0.8890 (tmm) cc_final: 0.8177 (tmm) REVERT: E 202 VAL cc_start: 0.8296 (t) cc_final: 0.8046 (m) REVERT: E 339 ASP cc_start: 0.8329 (m-30) cc_final: 0.7891 (m-30) REVERT: E 363 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6548 (pm20) REVERT: E 407 LEU cc_start: 0.8758 (mm) cc_final: 0.8546 (mm) REVERT: E 409 MET cc_start: 0.7864 (mmt) cc_final: 0.7134 (mmt) REVERT: E 498 ASN cc_start: 0.8421 (t0) cc_final: 0.8168 (t0) REVERT: E 536 GLU cc_start: 0.7823 (tp30) cc_final: 0.7430 (tt0) REVERT: E 622 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7526 (tpp80) REVERT: E 667 MET cc_start: 0.8243 (mmm) cc_final: 0.8040 (mmm) REVERT: E 709 MET cc_start: 0.7558 (mmm) cc_final: 0.7156 (tpt) REVERT: E 848 MET cc_start: 0.8025 (mmt) cc_final: 0.7800 (mmt) REVERT: F 26 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6722 (mm-40) outliers start: 132 outliers final: 97 residues processed: 856 average time/residue: 0.3525 time to fit residues: 471.7229 Evaluate side-chains 874 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 772 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 527 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 892 MET Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 117 optimal weight: 0.9990 chunk 315 optimal weight: 0.8980 chunk 69 optimal weight: 0.0050 chunk 205 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 115 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN B 796 GLN C 274 ASN D 692 ASN E 403 ASN E 467 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29880 Z= 0.177 Angle : 0.648 13.985 40550 Z= 0.321 Chirality : 0.043 0.237 4542 Planarity : 0.004 0.050 5250 Dihedral : 4.142 20.034 4040 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.17 % Allowed : 21.96 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3592 helix: 1.42 (0.13), residues: 1590 sheet: -0.28 (0.28), residues: 362 loop : -1.04 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 238 HIS 0.011 0.001 HIS D 378 PHE 0.032 0.001 PHE E 522 TYR 0.024 0.001 TYR E 17 ARG 0.008 0.000 ARG D 623 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 797 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8051 (tptm) cc_final: 0.7072 (tptm) REVERT: A 70 ASP cc_start: 0.7896 (m-30) cc_final: 0.7284 (m-30) REVERT: A 111 MET cc_start: 0.8731 (tmm) cc_final: 0.8132 (tmm) REVERT: A 147 ASP cc_start: 0.8512 (t0) cc_final: 0.8258 (t0) REVERT: A 157 GLU cc_start: 0.7654 (mp0) cc_final: 0.7420 (mp0) REVERT: A 167 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 257 ASP cc_start: 0.8181 (m-30) cc_final: 0.7926 (m-30) REVERT: A 371 MET cc_start: 0.6504 (mtm) cc_final: 0.6267 (mtt) REVERT: A 427 PHE cc_start: 0.8715 (p90) cc_final: 0.8494 (p90) REVERT: A 449 TYR cc_start: 0.7550 (m-80) cc_final: 0.7201 (m-80) REVERT: A 481 GLU cc_start: 0.8220 (mp0) cc_final: 0.7845 (mp0) REVERT: A 501 LEU cc_start: 0.8646 (tp) cc_final: 0.8361 (tp) REVERT: A 526 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7656 (ttp80) REVERT: A 552 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 582 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7784 (mmp-170) REVERT: A 636 PHE cc_start: 0.7835 (p90) cc_final: 0.7289 (p90) REVERT: A 641 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.7903 (mt) REVERT: A 668 ARG cc_start: 0.8638 (mtp85) cc_final: 0.8350 (mtm-85) REVERT: A 671 MET cc_start: 0.7701 (mmm) cc_final: 0.7307 (mmp) REVERT: A 709 MET cc_start: 0.8497 (pmm) cc_final: 0.8290 (pmm) REVERT: A 831 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 17 TYR cc_start: 0.7744 (p90) cc_final: 0.7191 (p90) REVERT: B 18 LEU cc_start: 0.8643 (tt) cc_final: 0.8419 (tp) REVERT: B 47 GLN cc_start: 0.7995 (pp30) cc_final: 0.7777 (tm-30) REVERT: B 70 ASP cc_start: 0.7755 (t0) cc_final: 0.7195 (t0) REVERT: B 291 MET cc_start: 0.8185 (tmm) cc_final: 0.7914 (tmm) REVERT: B 339 ASP cc_start: 0.8113 (m-30) cc_final: 0.7752 (m-30) REVERT: B 355 LEU cc_start: 0.7871 (mm) cc_final: 0.7626 (mm) REVERT: B 515 TYR cc_start: 0.8960 (t80) cc_final: 0.8534 (t80) REVERT: B 694 PHE cc_start: 0.7151 (p90) cc_final: 0.6833 (p90) REVERT: B 724 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7832 (mm-30) REVERT: B 742 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7122 (t) REVERT: B 747 GLU cc_start: 0.7728 (pp20) cc_final: 0.7489 (pp20) REVERT: B 861 VAL cc_start: 0.8557 (m) cc_final: 0.8222 (p) REVERT: B 869 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8622 (t) REVERT: C 314 THR cc_start: 0.6999 (OUTLIER) cc_final: 0.6703 (t) REVERT: D 40 MET cc_start: 0.8278 (mmm) cc_final: 0.8016 (mmp) REVERT: D 44 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7631 (mtt180) REVERT: D 66 LYS cc_start: 0.8359 (tptm) cc_final: 0.7988 (tptm) REVERT: D 99 ASP cc_start: 0.8201 (p0) cc_final: 0.7853 (p0) REVERT: D 111 MET cc_start: 0.8796 (tpp) cc_final: 0.8470 (tpp) REVERT: D 157 GLU cc_start: 0.7938 (mp0) cc_final: 0.7488 (mp0) REVERT: D 169 LYS cc_start: 0.8398 (mmmm) cc_final: 0.7939 (mmmt) REVERT: D 209 CYS cc_start: 0.7800 (t) cc_final: 0.7476 (t) REVERT: D 253 GLU cc_start: 0.7931 (mp0) cc_final: 0.7431 (mp0) REVERT: D 257 ASP cc_start: 0.8033 (m-30) cc_final: 0.7721 (m-30) REVERT: D 342 LYS cc_start: 0.8529 (ptpp) cc_final: 0.8158 (ptpp) REVERT: D 344 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.7870 (t80) REVERT: D 381 PHE cc_start: 0.8148 (m-80) cc_final: 0.7441 (m-80) REVERT: D 409 MET cc_start: 0.7032 (tpt) cc_final: 0.6762 (tpp) REVERT: D 552 LEU cc_start: 0.8716 (tt) cc_final: 0.8399 (tp) REVERT: D 573 TRP cc_start: 0.8209 (m100) cc_final: 0.7878 (m100) REVERT: D 620 MET cc_start: 0.8208 (tpp) cc_final: 0.7890 (tpp) REVERT: E 36 LEU cc_start: 0.8783 (mm) cc_final: 0.8484 (mm) REVERT: E 44 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7867 (ptm160) REVERT: E 111 MET cc_start: 0.8938 (tmm) cc_final: 0.8189 (tmm) REVERT: E 124 GLU cc_start: 0.7819 (pp20) cc_final: 0.7597 (pp20) REVERT: E 202 VAL cc_start: 0.8311 (t) cc_final: 0.8072 (m) REVERT: E 339 ASP cc_start: 0.8246 (m-30) cc_final: 0.7785 (m-30) REVERT: E 356 ASP cc_start: 0.5447 (p0) cc_final: 0.5047 (p0) REVERT: E 363 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6527 (pt0) REVERT: E 409 MET cc_start: 0.7962 (mmt) cc_final: 0.7162 (mmt) REVERT: E 411 ASN cc_start: 0.8274 (t0) cc_final: 0.7626 (t0) REVERT: E 498 ASN cc_start: 0.8379 (t0) cc_final: 0.8121 (t0) REVERT: E 524 MET cc_start: 0.8632 (mmm) cc_final: 0.8336 (mmm) REVERT: E 529 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7097 (ttt180) REVERT: E 622 ARG cc_start: 0.7593 (tpp80) cc_final: 0.7288 (tpp80) REVERT: E 642 ASN cc_start: 0.8707 (t0) cc_final: 0.8240 (t0) REVERT: E 709 MET cc_start: 0.7533 (mmm) cc_final: 0.7331 (tpt) REVERT: F 26 GLN cc_start: 0.7095 (mm-40) cc_final: 0.6685 (mm-40) outliers start: 101 outliers final: 69 residues processed: 855 average time/residue: 0.3494 time to fit residues: 466.2144 Evaluate side-chains 845 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 769 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 403 ASN Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 337 optimal weight: 0.6980 chunk 39 optimal weight: 0.0270 chunk 199 optimal weight: 0.8980 chunk 255 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 195 optimal weight: 0.0980 chunk 348 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN B 796 GLN C 274 ASN D 692 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29880 Z= 0.179 Angle : 0.664 14.387 40550 Z= 0.325 Chirality : 0.043 0.222 4542 Planarity : 0.004 0.051 5250 Dihedral : 4.031 19.692 4040 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 22.74 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3592 helix: 1.43 (0.13), residues: 1584 sheet: -0.12 (0.28), residues: 352 loop : -1.01 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 637 HIS 0.011 0.001 HIS D 378 PHE 0.036 0.001 PHE D 324 TYR 0.024 0.001 TYR E 17 ARG 0.009 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 780 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8076 (tptm) cc_final: 0.7123 (tptm) REVERT: A 70 ASP cc_start: 0.7908 (m-30) cc_final: 0.7270 (m-30) REVERT: A 111 MET cc_start: 0.8685 (tmm) cc_final: 0.8089 (tmm) REVERT: A 167 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 253 GLU cc_start: 0.8245 (mp0) cc_final: 0.7785 (mp0) REVERT: A 257 ASP cc_start: 0.8167 (m-30) cc_final: 0.7904 (m-30) REVERT: A 501 LEU cc_start: 0.8641 (tp) cc_final: 0.8382 (tp) REVERT: A 578 PHE cc_start: 0.7988 (m-80) cc_final: 0.7397 (m-80) REVERT: A 582 ARG cc_start: 0.8137 (mmp80) cc_final: 0.7661 (mmp80) REVERT: A 614 MET cc_start: 0.7704 (tpt) cc_final: 0.7433 (tpt) REVERT: A 636 PHE cc_start: 0.7666 (p90) cc_final: 0.7164 (p90) REVERT: A 641 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 668 ARG cc_start: 0.8615 (mtp85) cc_final: 0.8324 (mtm-85) REVERT: A 831 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 17 TYR cc_start: 0.7711 (p90) cc_final: 0.7156 (p90) REVERT: B 18 LEU cc_start: 0.8678 (tt) cc_final: 0.8430 (tp) REVERT: B 47 GLN cc_start: 0.7996 (pp30) cc_final: 0.7750 (tm-30) REVERT: B 70 ASP cc_start: 0.7520 (t0) cc_final: 0.7114 (t0) REVERT: B 291 MET cc_start: 0.8197 (tmm) cc_final: 0.7882 (tmm) REVERT: B 339 ASP cc_start: 0.8119 (m-30) cc_final: 0.7759 (m-30) REVERT: B 355 LEU cc_start: 0.7861 (mm) cc_final: 0.7625 (mm) REVERT: B 515 TYR cc_start: 0.8946 (t80) cc_final: 0.8518 (t80) REVERT: B 694 PHE cc_start: 0.7151 (p90) cc_final: 0.6856 (p90) REVERT: B 698 MET cc_start: 0.9191 (tpp) cc_final: 0.8987 (mmm) REVERT: B 724 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 742 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7113 (t) REVERT: B 747 GLU cc_start: 0.7715 (pp20) cc_final: 0.7480 (pp20) REVERT: B 792 ASP cc_start: 0.7647 (p0) cc_final: 0.7390 (p0) REVERT: B 861 VAL cc_start: 0.8564 (m) cc_final: 0.8228 (p) REVERT: D 40 MET cc_start: 0.8294 (mmm) cc_final: 0.8028 (mmp) REVERT: D 44 ARG cc_start: 0.7903 (mtt180) cc_final: 0.7584 (mtt180) REVERT: D 66 LYS cc_start: 0.8368 (tptm) cc_final: 0.8003 (tptm) REVERT: D 99 ASP cc_start: 0.8201 (p0) cc_final: 0.7872 (p0) REVERT: D 109 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7675 (tp30) REVERT: D 111 MET cc_start: 0.8774 (tpp) cc_final: 0.8470 (tpp) REVERT: D 169 LYS cc_start: 0.8342 (mmmm) cc_final: 0.7934 (mmmt) REVERT: D 209 CYS cc_start: 0.7772 (t) cc_final: 0.7479 (t) REVERT: D 253 GLU cc_start: 0.7909 (mp0) cc_final: 0.7464 (mp0) REVERT: D 257 ASP cc_start: 0.7976 (m-30) cc_final: 0.7697 (m-30) REVERT: D 342 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8176 (ptpp) REVERT: D 344 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7833 (t80) REVERT: D 381 PHE cc_start: 0.8147 (m-80) cc_final: 0.7928 (m-80) REVERT: D 409 MET cc_start: 0.6962 (tpt) cc_final: 0.6713 (tpp) REVERT: D 552 LEU cc_start: 0.8703 (tt) cc_final: 0.8392 (tp) REVERT: D 573 TRP cc_start: 0.8175 (m100) cc_final: 0.7838 (m100) REVERT: D 610 MET cc_start: 0.8161 (mtp) cc_final: 0.7911 (mtt) REVERT: D 620 MET cc_start: 0.8183 (tpp) cc_final: 0.7878 (tpp) REVERT: E 36 LEU cc_start: 0.8785 (mm) cc_final: 0.8474 (mm) REVERT: E 44 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7888 (ptm160) REVERT: E 111 MET cc_start: 0.8945 (tmm) cc_final: 0.8192 (tmm) REVERT: E 202 VAL cc_start: 0.8240 (t) cc_final: 0.8010 (m) REVERT: E 339 ASP cc_start: 0.8245 (m-30) cc_final: 0.7786 (m-30) REVERT: E 363 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: E 394 MET cc_start: 0.7941 (mtp) cc_final: 0.7732 (ttm) REVERT: E 409 MET cc_start: 0.7969 (mmt) cc_final: 0.7156 (mmt) REVERT: E 411 ASN cc_start: 0.8263 (t0) cc_final: 0.7568 (t0) REVERT: E 473 ARG cc_start: 0.8379 (ptt180) cc_final: 0.8136 (ptt-90) REVERT: E 498 ASN cc_start: 0.8374 (t0) cc_final: 0.8108 (t0) REVERT: E 642 ASN cc_start: 0.8703 (t0) cc_final: 0.8248 (t0) REVERT: F 26 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6658 (mm-40) outliers start: 102 outliers final: 77 residues processed: 837 average time/residue: 0.4162 time to fit residues: 544.2107 Evaluate side-chains 845 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 764 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 492 MET Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 215 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN D 692 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29880 Z= 0.216 Angle : 0.683 14.064 40550 Z= 0.335 Chirality : 0.044 0.232 4542 Planarity : 0.004 0.052 5250 Dihedral : 4.051 20.040 4040 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.39 % Allowed : 23.09 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3592 helix: 1.42 (0.13), residues: 1588 sheet: -0.15 (0.28), residues: 372 loop : -1.01 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 637 HIS 0.013 0.001 HIS D 378 PHE 0.025 0.001 PHE E 522 TYR 0.026 0.001 TYR E 17 ARG 0.008 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 778 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8103 (tptm) cc_final: 0.7147 (tptm) REVERT: A 70 ASP cc_start: 0.7917 (m-30) cc_final: 0.7280 (m-30) REVERT: A 111 MET cc_start: 0.8673 (tmm) cc_final: 0.8081 (tmm) REVERT: A 257 ASP cc_start: 0.8170 (m-30) cc_final: 0.7908 (m-30) REVERT: A 371 MET cc_start: 0.6484 (mtm) cc_final: 0.6175 (mtt) REVERT: A 449 TYR cc_start: 0.7501 (m-80) cc_final: 0.7142 (m-80) REVERT: A 481 GLU cc_start: 0.8234 (mp0) cc_final: 0.7820 (mp0) REVERT: A 501 LEU cc_start: 0.8673 (tp) cc_final: 0.8403 (tp) REVERT: A 582 ARG cc_start: 0.8183 (mmp80) cc_final: 0.7697 (mmp80) REVERT: A 614 MET cc_start: 0.7712 (tpt) cc_final: 0.7442 (tpt) REVERT: A 636 PHE cc_start: 0.7662 (p90) cc_final: 0.7224 (p90) REVERT: A 641 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8468 (mt) REVERT: A 667 MET cc_start: 0.8470 (tpp) cc_final: 0.7948 (tpp) REVERT: A 831 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 17 TYR cc_start: 0.7729 (p90) cc_final: 0.7158 (p90) REVERT: B 18 LEU cc_start: 0.8653 (tt) cc_final: 0.8449 (tp) REVERT: B 47 GLN cc_start: 0.7963 (pp30) cc_final: 0.7735 (tm-30) REVERT: B 193 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7538 (mm-30) REVERT: B 291 MET cc_start: 0.8198 (tmm) cc_final: 0.7865 (tmm) REVERT: B 339 ASP cc_start: 0.8123 (m-30) cc_final: 0.7756 (m-30) REVERT: B 355 LEU cc_start: 0.7868 (mm) cc_final: 0.7625 (mm) REVERT: B 515 TYR cc_start: 0.8956 (t80) cc_final: 0.8523 (t80) REVERT: B 724 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 747 GLU cc_start: 0.7734 (pp20) cc_final: 0.7533 (pp20) REVERT: B 793 ASP cc_start: 0.8248 (t70) cc_final: 0.7911 (t0) REVERT: B 861 VAL cc_start: 0.8573 (m) cc_final: 0.8366 (t) REVERT: D 40 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8043 (mmp) REVERT: D 44 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7588 (mtt180) REVERT: D 66 LYS cc_start: 0.8391 (tptm) cc_final: 0.8024 (tptm) REVERT: D 99 ASP cc_start: 0.8210 (p0) cc_final: 0.7890 (p0) REVERT: D 109 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7706 (tp30) REVERT: D 111 MET cc_start: 0.8765 (tpp) cc_final: 0.8449 (tpp) REVERT: D 169 LYS cc_start: 0.8345 (mmmm) cc_final: 0.7940 (mmmt) REVERT: D 209 CYS cc_start: 0.7839 (t) cc_final: 0.7548 (t) REVERT: D 253 GLU cc_start: 0.7893 (mp0) cc_final: 0.7465 (mp0) REVERT: D 324 PHE cc_start: 0.6787 (p90) cc_final: 0.6309 (p90) REVERT: D 342 LYS cc_start: 0.8583 (ptpp) cc_final: 0.8231 (ptpp) REVERT: D 344 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7840 (t80) REVERT: D 409 MET cc_start: 0.6982 (tpt) cc_final: 0.6725 (tpp) REVERT: D 573 TRP cc_start: 0.8264 (m100) cc_final: 0.7952 (m100) REVERT: D 610 MET cc_start: 0.8241 (mtp) cc_final: 0.8031 (mtt) REVERT: D 620 MET cc_start: 0.8212 (tpp) cc_final: 0.7902 (tpp) REVERT: D 744 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: E 36 LEU cc_start: 0.8828 (mm) cc_final: 0.8512 (mm) REVERT: E 44 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7857 (ptm160) REVERT: E 81 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7853 (ptmm) REVERT: E 111 MET cc_start: 0.8925 (tmm) cc_final: 0.8170 (tmm) REVERT: E 339 ASP cc_start: 0.8264 (m-30) cc_final: 0.7803 (m-30) REVERT: E 363 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6767 (pt0) REVERT: E 394 MET cc_start: 0.7924 (mtp) cc_final: 0.7718 (ttm) REVERT: E 409 MET cc_start: 0.7982 (mmt) cc_final: 0.7146 (mmt) REVERT: E 411 ASN cc_start: 0.8310 (t0) cc_final: 0.7605 (t0) REVERT: E 498 ASN cc_start: 0.8382 (t0) cc_final: 0.8114 (t0) REVERT: E 529 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7180 (ttt180) REVERT: E 536 GLU cc_start: 0.7895 (tp30) cc_final: 0.7536 (tt0) REVERT: E 642 ASN cc_start: 0.8710 (t0) cc_final: 0.8352 (t0) REVERT: F 26 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6722 (mm-40) outliers start: 108 outliers final: 91 residues processed: 840 average time/residue: 0.4217 time to fit residues: 554.4060 Evaluate side-chains 858 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 762 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 317 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 304 optimal weight: 0.7980 chunk 325 optimal weight: 4.9990 chunk 195 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 255 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN D 692 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29880 Z= 0.196 Angle : 0.706 14.392 40550 Z= 0.344 Chirality : 0.044 0.240 4542 Planarity : 0.004 0.051 5250 Dihedral : 4.005 19.476 4040 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.11 % Allowed : 24.03 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3592 helix: 1.44 (0.13), residues: 1580 sheet: -0.09 (0.28), residues: 370 loop : -1.00 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 637 HIS 0.012 0.001 HIS D 378 PHE 0.026 0.001 PHE E 522 TYR 0.025 0.001 TYR E 17 ARG 0.010 0.000 ARG D 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 768 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8086 (tptm) cc_final: 0.7136 (tptm) REVERT: A 70 ASP cc_start: 0.7920 (m-30) cc_final: 0.7278 (m-30) REVERT: A 111 MET cc_start: 0.8643 (tmm) cc_final: 0.8068 (tmm) REVERT: A 167 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 257 ASP cc_start: 0.8168 (m-30) cc_final: 0.7894 (m-30) REVERT: A 449 TYR cc_start: 0.7454 (m-80) cc_final: 0.7091 (m-80) REVERT: A 501 LEU cc_start: 0.8666 (tp) cc_final: 0.8395 (tp) REVERT: A 526 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7668 (ttp80) REVERT: A 582 ARG cc_start: 0.8173 (mmp80) cc_final: 0.7681 (mmp80) REVERT: A 641 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8361 (mm) REVERT: A 667 MET cc_start: 0.8416 (tpp) cc_final: 0.8108 (tpp) REVERT: B 17 TYR cc_start: 0.7742 (p90) cc_final: 0.7162 (p90) REVERT: B 18 LEU cc_start: 0.8663 (tt) cc_final: 0.8444 (tp) REVERT: B 47 GLN cc_start: 0.7952 (pp30) cc_final: 0.7728 (tm-30) REVERT: B 70 ASP cc_start: 0.7626 (t0) cc_final: 0.6768 (t0) REVERT: B 291 MET cc_start: 0.8189 (tmm) cc_final: 0.7840 (tmm) REVERT: B 339 ASP cc_start: 0.8109 (m-30) cc_final: 0.7736 (m-30) REVERT: B 355 LEU cc_start: 0.7889 (mm) cc_final: 0.7637 (mm) REVERT: B 515 TYR cc_start: 0.8943 (t80) cc_final: 0.8525 (t80) REVERT: B 674 SER cc_start: 0.8370 (m) cc_final: 0.7975 (p) REVERT: B 694 PHE cc_start: 0.7189 (p90) cc_final: 0.6914 (p90) REVERT: B 724 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 861 VAL cc_start: 0.8570 (m) cc_final: 0.8264 (p) REVERT: D 40 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8032 (mmp) REVERT: D 44 ARG cc_start: 0.7913 (mtt180) cc_final: 0.7585 (mtt180) REVERT: D 66 LYS cc_start: 0.8370 (tptm) cc_final: 0.8008 (tptm) REVERT: D 99 ASP cc_start: 0.8203 (p0) cc_final: 0.7866 (p0) REVERT: D 109 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7891 (tp30) REVERT: D 111 MET cc_start: 0.8769 (tpp) cc_final: 0.8451 (tpp) REVERT: D 169 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7981 (mmmt) REVERT: D 209 CYS cc_start: 0.7800 (t) cc_final: 0.7504 (t) REVERT: D 324 PHE cc_start: 0.6697 (p90) cc_final: 0.6225 (p90) REVERT: D 344 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7740 (t80) REVERT: D 409 MET cc_start: 0.6921 (tpt) cc_final: 0.6649 (tpp) REVERT: D 573 TRP cc_start: 0.8244 (m100) cc_final: 0.7935 (m100) REVERT: D 620 MET cc_start: 0.8180 (tpp) cc_final: 0.7875 (tpp) REVERT: D 744 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: E 36 LEU cc_start: 0.8787 (mm) cc_final: 0.8474 (mm) REVERT: E 44 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7850 (ptm160) REVERT: E 81 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7806 (ptmm) REVERT: E 98 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7648 (tpt90) REVERT: E 111 MET cc_start: 0.8919 (tmm) cc_final: 0.8167 (tmm) REVERT: E 339 ASP cc_start: 0.8255 (m-30) cc_final: 0.7789 (m-30) REVERT: E 363 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6715 (pt0) REVERT: E 409 MET cc_start: 0.7984 (mmt) cc_final: 0.7136 (mmt) REVERT: E 411 ASN cc_start: 0.8305 (t0) cc_final: 0.7597 (t0) REVERT: E 498 ASN cc_start: 0.8373 (t0) cc_final: 0.8106 (t0) REVERT: E 536 GLU cc_start: 0.7883 (tp30) cc_final: 0.7526 (tt0) REVERT: E 642 ASN cc_start: 0.8691 (t0) cc_final: 0.8272 (t0) REVERT: E 884 MET cc_start: 0.6607 (tpt) cc_final: 0.6246 (tpt) REVERT: F 26 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6678 (mm-40) outliers start: 99 outliers final: 87 residues processed: 825 average time/residue: 0.4112 time to fit residues: 529.3814 Evaluate side-chains 862 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 770 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 655 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 744 TYR Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 869 VAL Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 265 TRP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain E residue 886 ILE Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 213 optimal weight: 10.0000 chunk 343 optimal weight: 0.0770 chunk 209 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 239 optimal weight: 0.8980 chunk 360 optimal weight: 3.9990 chunk 331 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 221 optimal weight: 0.1980 chunk 176 optimal weight: 0.6980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29880 Z= 0.192 Angle : 0.708 14.590 40550 Z= 0.343 Chirality : 0.043 0.244 4542 Planarity : 0.004 0.050 5250 Dihedral : 3.929 19.499 4040 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.85 % Allowed : 24.56 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3592 helix: 1.46 (0.13), residues: 1576 sheet: -0.05 (0.28), residues: 370 loop : -0.97 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 637 HIS 0.012 0.001 HIS D 378 PHE 0.026 0.001 PHE D 636 TYR 0.025 0.001 TYR E 17 ARG 0.011 0.000 ARG E 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7184 Ramachandran restraints generated. 3592 Oldfield, 0 Emsley, 3592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 781 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8045 (mmm) cc_final: 0.7807 (mmm) REVERT: A 66 LYS cc_start: 0.8085 (tptm) cc_final: 0.7665 (tptm) REVERT: A 111 MET cc_start: 0.8623 (tmm) cc_final: 0.8072 (tmm) REVERT: A 147 ASP cc_start: 0.8503 (t0) cc_final: 0.8291 (t0) REVERT: A 167 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 253 GLU cc_start: 0.8224 (mp0) cc_final: 0.7554 (mp0) REVERT: A 257 ASP cc_start: 0.8139 (m-30) cc_final: 0.7804 (m-30) REVERT: A 518 SER cc_start: 0.8726 (m) cc_final: 0.8143 (p) REVERT: A 526 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7616 (ttp80) REVERT: A 552 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 582 ARG cc_start: 0.8149 (mmp80) cc_final: 0.7708 (mmp80) REVERT: A 589 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8151 (mtp85) REVERT: A 641 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8410 (mm) REVERT: A 667 MET cc_start: 0.8426 (tpp) cc_final: 0.7957 (tpp) REVERT: A 671 MET cc_start: 0.7606 (mmm) cc_final: 0.7297 (mmp) REVERT: A 766 MET cc_start: 0.7844 (mmm) cc_final: 0.7585 (mmp) REVERT: A 831 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7988 (tm-30) REVERT: B 17 TYR cc_start: 0.7735 (p90) cc_final: 0.7150 (p90) REVERT: B 18 LEU cc_start: 0.8658 (tt) cc_final: 0.8423 (tp) REVERT: B 36 LEU cc_start: 0.8935 (mm) cc_final: 0.8646 (mm) REVERT: B 291 MET cc_start: 0.8162 (tmm) cc_final: 0.7812 (tmm) REVERT: B 339 ASP cc_start: 0.8084 (m-30) cc_final: 0.7707 (m-30) REVERT: B 355 LEU cc_start: 0.7848 (mm) cc_final: 0.7619 (mm) REVERT: B 515 TYR cc_start: 0.8919 (t80) cc_final: 0.8536 (t80) REVERT: B 674 SER cc_start: 0.8257 (m) cc_final: 0.7844 (p) REVERT: B 694 PHE cc_start: 0.7177 (p90) cc_final: 0.6884 (p90) REVERT: B 724 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 861 VAL cc_start: 0.8544 (m) cc_final: 0.8238 (p) REVERT: D 40 MET cc_start: 0.8259 (mmm) cc_final: 0.8015 (mmp) REVERT: D 44 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7512 (mtt180) REVERT: D 66 LYS cc_start: 0.8354 (tptm) cc_final: 0.7994 (tptm) REVERT: D 99 ASP cc_start: 0.8216 (p0) cc_final: 0.7884 (p0) REVERT: D 109 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7863 (tp30) REVERT: D 111 MET cc_start: 0.8773 (tpp) cc_final: 0.8454 (tpp) REVERT: D 169 LYS cc_start: 0.8311 (mmmm) cc_final: 0.7927 (mmmt) REVERT: D 209 CYS cc_start: 0.7726 (t) cc_final: 0.7421 (t) REVERT: D 324 PHE cc_start: 0.6686 (p90) cc_final: 0.6247 (p90) REVERT: D 344 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7820 (t80) REVERT: D 409 MET cc_start: 0.6876 (tpt) cc_final: 0.6604 (tpp) REVERT: D 573 TRP cc_start: 0.8221 (m100) cc_final: 0.7905 (m100) REVERT: E 36 LEU cc_start: 0.8761 (mm) cc_final: 0.8443 (mm) REVERT: E 44 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7897 (ptm160) REVERT: E 81 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7779 (ptmm) REVERT: E 111 MET cc_start: 0.8969 (tmm) cc_final: 0.8169 (tmm) REVERT: E 339 ASP cc_start: 0.8191 (m-30) cc_final: 0.7761 (m-30) REVERT: E 348 MET cc_start: 0.8111 (mmt) cc_final: 0.7877 (mtp) REVERT: E 363 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6680 (pt0) REVERT: E 411 ASN cc_start: 0.8329 (t0) cc_final: 0.8108 (t0) REVERT: E 498 ASN cc_start: 0.8369 (t0) cc_final: 0.8101 (t0) REVERT: E 642 ASN cc_start: 0.8648 (t0) cc_final: 0.8233 (t0) REVERT: E 807 ARG cc_start: 0.8473 (mpp-170) cc_final: 0.8117 (mpp-170) REVERT: E 884 MET cc_start: 0.6576 (tpt) cc_final: 0.6209 (tpt) REVERT: F 26 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6600 (mm-40) outliers start: 91 outliers final: 78 residues processed: 834 average time/residue: 0.4191 time to fit residues: 543.9389 Evaluate side-chains 846 residues out of total 3188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 764 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 265 TRP Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 881 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 527 PHE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 795 LEU Chi-restraints excluded: chain D residue 866 ILE Chi-restraints excluded: chain D residue 890 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 363 GLU Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 GLU Chi-restraints excluded: chain E residue 527 PHE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 575 SER Chi-restraints excluded: chain E residue 772 VAL Chi-restraints excluded: chain E residue 867 LEU Chi-restraints excluded: chain F residue 328 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 228 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 264 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 ASN C 274 ASN D 146 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS E 244 HIS E 523 HIS E 539 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075500 restraints weight = 69996.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078134 restraints weight = 32672.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.079828 restraints weight = 19026.714| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29880 Z= 0.303 Angle : 0.752 14.213 40550 Z= 0.372 Chirality : 0.046 0.238 4542 Planarity : 0.004 0.048 5250 Dihedral : 4.185 21.015 4040 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.20 % Allowed : 24.31 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3592 helix: 1.38 (0.13), residues: 1584 sheet: -0.25 (0.27), residues: 392 loop : -1.00 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 637 HIS 0.013 0.001 HIS D 378 PHE 0.030 0.002 PHE D 522 TYR 0.028 0.002 TYR E 17 ARG 0.007 0.000 ARG D 623 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8209.05 seconds wall clock time: 185 minutes 11.43 seconds (11111.43 seconds total)