Starting phenix.real_space_refine on Sun Feb 18 08:09:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yx9_6856/02_2024/5yx9_6856_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yx9_6856/02_2024/5yx9_6856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yx9_6856/02_2024/5yx9_6856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yx9_6856/02_2024/5yx9_6856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yx9_6856/02_2024/5yx9_6856_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yx9_6856/02_2024/5yx9_6856_neut.pdb" } resolution = 3.8 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= 0.018 sd= 0.097 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 136 5.16 5 C 13868 2.51 5 N 3536 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "C ARG 544": "NH1" <-> "NH2" Residue "C ARG 609": "NH1" <-> "NH2" Residue "C ARG 629": "NH1" <-> "NH2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 240": "NH1" <-> "NH2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ARG 609": "NH1" <-> "NH2" Residue "D ARG 629": "NH1" <-> "NH2" Residue "D ARG 758": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21392 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5348 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 656} Chain breaks: 6 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5348 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 656} Chain breaks: 6 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5348 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 656} Chain breaks: 6 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5348 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 656} Chain breaks: 6 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 11.14, per 1000 atoms: 0.52 Number of scatterers: 21392 At special positions: 0 Unit cell: (131.67, 131.67, 167.58, 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 136 16.00 O 3852 8.00 N 3536 7.00 C 13868 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: 8.74 Conformation dependent library (CDL) restraints added in 4.0 seconds 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG A 271 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 463 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR A 612 " --> pdb=" O ARG A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN A 721 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 854 through 876 Processing helix chain 'A' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 160 through 172 Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 364 through 372 Processing helix chain 'B' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 379' Processing helix chain 'B' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU B 393 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 463 " --> pdb=" O MET B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR B 612 " --> pdb=" O ARG B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY B 628 " --> pdb=" O GLN B 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 629 " --> pdb=" O ILE B 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS B 676 " --> pdb=" O GLU B 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN B 721 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 854 through 876 Processing helix chain 'B' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU B 884 " --> pdb=" O ASN B 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 121 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 160 through 172 Processing helix chain 'C' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 256 through 263 Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG C 271 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 311 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 364 through 372 Processing helix chain 'C' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 379' Processing helix chain 'C' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR C 515 " --> pdb=" O LYS C 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 516 " --> pdb=" O GLU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 522 Processing helix chain 'C' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR C 612 " --> pdb=" O ARG C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 629 " --> pdb=" O ILE C 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS C 636 " --> pdb=" O LYS C 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE C 637 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 Processing helix chain 'C' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN C 721 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 733 " --> pdb=" O SER C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 854 through 876 Processing helix chain 'C' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU C 884 " --> pdb=" O ASN C 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.618A pdb=" N VAL D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 143 removed outlier: 3.708A pdb=" N ASN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 173 through 182 removed outlier: 3.518A pdb=" N SER D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 256 through 263 Processing helix chain 'D' and resid 267 through 281 removed outlier: 3.826A pdb=" N ARG D 271 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.292A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 4.144A pdb=" N THR D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 335 removed outlier: 3.718A pdb=" N LEU D 335 " --> pdb=" O GLY D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 374 through 379 removed outlier: 4.012A pdb=" N VAL D 378 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 379' Processing helix chain 'D' and resid 380 through 393 removed outlier: 3.552A pdb=" N GLU D 393 " --> pdb=" O SER D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 3.717A pdb=" N PHE D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 4.502A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 437 removed outlier: 3.548A pdb=" N ARG D 437 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 463 removed outlier: 3.534A pdb=" N LYS D 442 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 443 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP D 463 " --> pdb=" O MET D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 516 removed outlier: 4.129A pdb=" N THR D 515 " --> pdb=" O LYS D 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 522 Processing helix chain 'D' and resid 524 through 558 removed outlier: 4.040A pdb=" N PHE D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 608 removed outlier: 3.778A pdb=" N ILE D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.540A pdb=" N TYR D 612 " --> pdb=" O ARG D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 657 removed outlier: 3.895A pdb=" N GLY D 628 " --> pdb=" O GLN D 624 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 629 " --> pdb=" O ILE D 625 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 636 " --> pdb=" O LYS D 632 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE D 637 " --> pdb=" O ASP D 633 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE D 640 " --> pdb=" O LYS D 636 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 680 removed outlier: 3.815A pdb=" N LYS D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 Processing helix chain 'D' and resid 697 through 733 removed outlier: 3.693A pdb=" N ASN D 721 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 752 Processing helix chain 'D' and resid 854 through 876 Processing helix chain 'D' and resid 880 through 921 removed outlier: 3.674A pdb=" N LEU D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) 1396 hydrogen bonds defined for protein. 4140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.07 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6764 1.34 - 1.46: 5004 1.46 - 1.58: 9852 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 21848 Sorted by residual: bond pdb=" CZ TYR D 521 " pdb=" OH TYR D 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CZ TYR A 521 " pdb=" OH TYR A 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CZ TYR B 521 " pdb=" OH TYR B 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CZ TYR C 521 " pdb=" OH TYR C 521 " ideal model delta sigma weight residual 1.376 1.420 -0.044 2.10e-02 2.27e+03 4.29e+00 bond pdb=" CA TYR A 521 " pdb=" CB TYR A 521 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.56e-02 4.11e+03 2.53e+00 ... (remaining 21843 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 496 106.74 - 113.56: 11944 113.56 - 120.38: 8892 120.38 - 127.21: 7964 127.21 - 134.03: 224 Bond angle restraints: 29520 Sorted by residual: angle pdb=" N GLN C 516 " pdb=" CA GLN C 516 " pdb=" C GLN C 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" N GLN D 516 " pdb=" CA GLN D 516 " pdb=" C GLN D 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" N GLN B 516 " pdb=" CA GLN B 516 " pdb=" C GLN B 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" N GLN A 516 " pdb=" CA GLN A 516 " pdb=" C GLN A 516 " ideal model delta sigma weight residual 109.07 119.11 -10.04 1.61e+00 3.86e-01 3.89e+01 angle pdb=" C GLU D 666 " pdb=" N ALA D 667 " pdb=" CA ALA D 667 " ideal model delta sigma weight residual 121.53 130.59 -9.06 2.25e+00 1.98e-01 1.62e+01 ... (remaining 29515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 11816 17.05 - 34.11: 892 34.11 - 51.16: 260 51.16 - 68.22: 60 68.22 - 85.27: 16 Dihedral angle restraints: 13044 sinusoidal: 5104 harmonic: 7940 Sorted by residual: dihedral pdb=" CA GLY B 189 " pdb=" C GLY B 189 " pdb=" N LYS B 190 " pdb=" CA LYS B 190 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY C 189 " pdb=" C GLY C 189 " pdb=" N LYS C 190 " pdb=" CA LYS C 190 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A 189 " pdb=" C GLY A 189 " pdb=" N LYS A 190 " pdb=" CA LYS A 190 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2832 0.055 - 0.110: 404 0.110 - 0.166: 56 0.166 - 0.221: 4 0.221 - 0.276: 4 Chirality restraints: 3300 Sorted by residual: chirality pdb=" CA GLN A 516 " pdb=" N GLN A 516 " pdb=" C GLN A 516 " pdb=" CB GLN A 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLN D 516 " pdb=" N GLN D 516 " pdb=" C GLN D 516 " pdb=" CB GLN D 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA GLN C 516 " pdb=" N GLN C 516 " pdb=" C GLN C 516 " pdb=" CB GLN C 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3297 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 521 " -0.027 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR A 521 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 521 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 521 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 521 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 521 " 0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A 521 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 521 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 521 " -0.027 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR D 521 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 521 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 521 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 521 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR D 521 " 0.056 2.00e-02 2.50e+03 pdb=" CZ TYR D 521 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR D 521 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 521 " 0.027 2.00e-02 2.50e+03 4.27e-02 3.65e+01 pdb=" CG TYR B 521 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 521 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 521 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 521 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR B 521 " -0.056 2.00e-02 2.50e+03 pdb=" CZ TYR B 521 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 521 " 0.083 2.00e-02 2.50e+03 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4140 2.77 - 3.31: 21196 3.31 - 3.84: 33704 3.84 - 4.37: 37856 4.37 - 4.90: 64160 Nonbonded interactions: 161056 Sorted by model distance: nonbonded pdb=" O SER C 552 " pdb=" OG SER C 556 " model vdw 2.243 2.440 nonbonded pdb=" O SER D 552 " pdb=" OG SER D 556 " model vdw 2.243 2.440 nonbonded pdb=" O SER B 552 " pdb=" OG SER B 556 " model vdw 2.243 2.440 nonbonded pdb=" O SER A 552 " pdb=" OG SER A 556 " model vdw 2.243 2.440 nonbonded pdb=" CG2 ILE C 513 " pdb=" CE1 TYR C 521 " model vdw 2.244 3.760 ... (remaining 161051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.490 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: 3.070 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 56.090 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 0.044 21848 Z= 0.211 Angle : 0.684 10.044 29520 Z= 0.381 Chirality : 0.041 0.276 3300 Planarity : 0.004 0.054 3712 Dihedral : 14.253 85.272 7884 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 2.14 % Allowed : 11.94 % Favored : 85.92 % 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: -3.27 (0.13), residues: 2644 helix: -1.80 (0.10), residues: 1916 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 750 HIS 0.008 0.001 HIS C 218 PHE 0.014 0.001 PHE D 731 TYR 0.083 0.003 TYR A 521 ARG 0.003 0.000 ARG B 895 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 600 time to evaluate : 2.437 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 190 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8046 (tppt) REVERT: A 295 MET cc_start: 0.9251 (tpt) cc_final: 0.8397 (tpp) REVERT: A 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8813 (tt) REVERT: A 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8775 (p0) REVERT: A 311 GLU cc_start: 0.8575 (tt0) cc_final: 0.8008 (tt0) REVERT: A 315 LYS cc_start: 0.8795 (tttt) cc_final: 0.8400 (pttp) REVERT: A 327 ASP cc_start: 0.9519 (t70) cc_final: 0.9271 (t0) REVERT: A 336 CYS cc_start: 0.8927 (p) cc_final: 0.8719 (p) REVERT: A 432 MET cc_start: 0.9194 (mmm) cc_final: 0.8846 (mmt) REVERT: A 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9066 (tt) REVERT: A 507 TRP cc_start: 0.8983 (t-100) cc_final: 0.8705 (t-100) REVERT: A 521 TYR cc_start: 0.7924 (t80) cc_final: 0.7411 (t80) REVERT: A 599 TYR cc_start: 0.9433 (t80) cc_final: 0.9031 (t80) REVERT: A 633 ASP cc_start: 0.9071 (m-30) cc_final: 0.8531 (m-30) REVERT: A 649 MET cc_start: 0.9452 (tmm) cc_final: 0.9136 (ppp) REVERT: A 687 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9112 (tp30) REVERT: A 722 MET cc_start: 0.9406 (mmm) cc_final: 0.9125 (tpp) REVERT: A 897 GLU cc_start: 0.9189 (tt0) cc_final: 0.8452 (tp30) REVERT: A 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8341 (tm-30) REVERT: B 190 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8047 (tppt) REVERT: B 295 MET cc_start: 0.9250 (tpt) cc_final: 0.8399 (tpp) REVERT: B 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8813 (tt) REVERT: B 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8774 (p0) REVERT: B 311 GLU cc_start: 0.8571 (tt0) cc_final: 0.8009 (tt0) REVERT: B 315 LYS cc_start: 0.8796 (tttt) cc_final: 0.8401 (pttp) REVERT: B 327 ASP cc_start: 0.9519 (t70) cc_final: 0.9272 (t0) REVERT: B 336 CYS cc_start: 0.8927 (p) cc_final: 0.8718 (p) REVERT: B 432 MET cc_start: 0.9193 (mmm) cc_final: 0.8843 (mmt) REVERT: B 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9066 (tt) REVERT: B 507 TRP cc_start: 0.8982 (t-100) cc_final: 0.8705 (t-100) REVERT: B 521 TYR cc_start: 0.7922 (t80) cc_final: 0.7405 (t80) REVERT: B 599 TYR cc_start: 0.9432 (t80) cc_final: 0.9032 (t80) REVERT: B 633 ASP cc_start: 0.9072 (m-30) cc_final: 0.8530 (m-30) REVERT: B 649 MET cc_start: 0.9453 (tmm) cc_final: 0.9137 (ppp) REVERT: B 687 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9112 (tp30) REVERT: B 722 MET cc_start: 0.9403 (mmm) cc_final: 0.9122 (tpp) REVERT: B 897 GLU cc_start: 0.9188 (tt0) cc_final: 0.8448 (tp30) REVERT: B 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8339 (tm-30) REVERT: C 190 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8049 (tppt) REVERT: C 295 MET cc_start: 0.9250 (tpt) cc_final: 0.8398 (tpp) REVERT: C 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8811 (tt) REVERT: C 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8774 (p0) REVERT: C 311 GLU cc_start: 0.8571 (tt0) cc_final: 0.8007 (tt0) REVERT: C 315 LYS cc_start: 0.8794 (tttt) cc_final: 0.8399 (pttp) REVERT: C 327 ASP cc_start: 0.9519 (t70) cc_final: 0.9272 (t0) REVERT: C 336 CYS cc_start: 0.8931 (p) cc_final: 0.8723 (p) REVERT: C 432 MET cc_start: 0.9193 (mmm) cc_final: 0.8843 (mmt) REVERT: C 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9066 (tt) REVERT: C 507 TRP cc_start: 0.8982 (t-100) cc_final: 0.8703 (t-100) REVERT: C 521 TYR cc_start: 0.7922 (t80) cc_final: 0.7407 (t80) REVERT: C 599 TYR cc_start: 0.9432 (t80) cc_final: 0.9031 (t80) REVERT: C 633 ASP cc_start: 0.9073 (m-30) cc_final: 0.8533 (m-30) REVERT: C 649 MET cc_start: 0.9453 (tmm) cc_final: 0.9136 (ppp) REVERT: C 687 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9113 (tp30) REVERT: C 722 MET cc_start: 0.9405 (mmm) cc_final: 0.9121 (tpp) REVERT: C 897 GLU cc_start: 0.9189 (tt0) cc_final: 0.8450 (tp30) REVERT: C 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8340 (tm-30) REVERT: D 190 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8048 (tppt) REVERT: D 295 MET cc_start: 0.9250 (tpt) cc_final: 0.8396 (tpp) REVERT: D 307 LEU cc_start: 0.9513 (mp) cc_final: 0.8813 (tt) REVERT: D 309 ASN cc_start: 0.9451 (m-40) cc_final: 0.8776 (p0) REVERT: D 311 GLU cc_start: 0.8573 (tt0) cc_final: 0.8007 (tt0) REVERT: D 315 LYS cc_start: 0.8795 (tttt) cc_final: 0.8401 (pttp) REVERT: D 327 ASP cc_start: 0.9517 (t70) cc_final: 0.9271 (t0) REVERT: D 336 CYS cc_start: 0.8925 (p) cc_final: 0.8721 (p) REVERT: D 432 MET cc_start: 0.9193 (mmm) cc_final: 0.8846 (mmt) REVERT: D 456 LEU cc_start: 0.9304 (mt) cc_final: 0.9067 (tt) REVERT: D 507 TRP cc_start: 0.8982 (t-100) cc_final: 0.8704 (t-100) REVERT: D 521 TYR cc_start: 0.7923 (t80) cc_final: 0.7409 (t80) REVERT: D 599 TYR cc_start: 0.9431 (t80) cc_final: 0.9030 (t80) REVERT: D 633 ASP cc_start: 0.9072 (m-30) cc_final: 0.8532 (m-30) REVERT: D 649 MET cc_start: 0.9453 (tmm) cc_final: 0.9136 (ppp) REVERT: D 687 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9113 (tp30) REVERT: D 722 MET cc_start: 0.9405 (mmm) cc_final: 0.9122 (tpp) REVERT: D 897 GLU cc_start: 0.9191 (tt0) cc_final: 0.8445 (tp30) REVERT: D 900 GLU cc_start: 0.8873 (tp30) cc_final: 0.8341 (tm-30) outliers start: 48 outliers final: 17 residues processed: 624 average time/residue: 0.3292 time to fit residues: 309.7396 Evaluate side-chains 373 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 352 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 190 LYS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 608 SER Chi-restraints excluded: chain D residue 901 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 137 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 156 optimal weight: 0.0370 chunk 243 optimal weight: 1.9990 overall best weight: 3.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 732 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 732 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21848 Z= 0.259 Angle : 0.655 7.968 29520 Z= 0.336 Chirality : 0.040 0.188 3300 Planarity : 0.005 0.042 3712 Dihedral : 5.927 46.187 2931 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.94 % Allowed : 19.21 % Favored : 77.85 % 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: -0.49 (0.15), residues: 2644 helix: 0.62 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : -3.12 (0.18), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 750 HIS 0.007 0.001 HIS A 218 PHE 0.015 0.001 PHE A 731 TYR 0.015 0.002 TYR B 658 ARG 0.003 0.000 ARG B 853 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 381 time to evaluate : 2.579 Fit side-chains REVERT: A 87 MET cc_start: 0.7731 (tmm) cc_final: 0.7235 (tmm) REVERT: A 253 CYS cc_start: 0.9129 (t) cc_final: 0.8887 (p) REVERT: A 309 ASN cc_start: 0.9404 (m-40) cc_final: 0.8701 (p0) REVERT: A 311 GLU cc_start: 0.8612 (tt0) cc_final: 0.7910 (tt0) REVERT: A 315 LYS cc_start: 0.8738 (tttt) cc_final: 0.8299 (pttp) REVERT: A 327 ASP cc_start: 0.9456 (t70) cc_final: 0.9244 (t0) REVERT: A 365 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8320 (ttm110) REVERT: A 436 MET cc_start: 0.9348 (mmm) cc_final: 0.9142 (mmm) REVERT: A 494 MET cc_start: 0.9121 (mmp) cc_final: 0.8187 (mtm) REVERT: A 510 CYS cc_start: 0.8646 (m) cc_final: 0.8172 (t) REVERT: A 533 MET cc_start: 0.9125 (tmm) cc_final: 0.8770 (tmm) REVERT: A 607 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8796 (t80) REVERT: A 633 ASP cc_start: 0.9083 (m-30) cc_final: 0.8639 (m-30) REVERT: A 649 MET cc_start: 0.9365 (tmm) cc_final: 0.9123 (ppp) REVERT: A 670 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 687 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8778 (pt0) REVERT: A 701 GLU cc_start: 0.9329 (tt0) cc_final: 0.8917 (pt0) REVERT: A 715 MET cc_start: 0.9155 (tmm) cc_final: 0.8886 (tmm) REVERT: A 900 GLU cc_start: 0.8895 (tp30) cc_final: 0.8465 (tm-30) REVERT: B 87 MET cc_start: 0.7729 (tmm) cc_final: 0.7235 (tmm) REVERT: B 253 CYS cc_start: 0.9133 (t) cc_final: 0.8889 (p) REVERT: B 309 ASN cc_start: 0.9404 (m-40) cc_final: 0.8702 (p0) REVERT: B 311 GLU cc_start: 0.8610 (tt0) cc_final: 0.7906 (tt0) REVERT: B 315 LYS cc_start: 0.8738 (tttt) cc_final: 0.8299 (pttp) REVERT: B 327 ASP cc_start: 0.9457 (t70) cc_final: 0.9245 (t0) REVERT: B 365 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8320 (ttm110) REVERT: B 436 MET cc_start: 0.9348 (mmm) cc_final: 0.9144 (mmm) REVERT: B 494 MET cc_start: 0.9121 (mmp) cc_final: 0.8187 (mtm) REVERT: B 510 CYS cc_start: 0.8643 (m) cc_final: 0.8169 (t) REVERT: B 533 MET cc_start: 0.9126 (tmm) cc_final: 0.8770 (tmm) REVERT: B 607 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8795 (t80) REVERT: B 633 ASP cc_start: 0.9085 (m-30) cc_final: 0.8641 (m-30) REVERT: B 649 MET cc_start: 0.9366 (tmm) cc_final: 0.9125 (ppp) REVERT: B 670 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8611 (p) REVERT: B 687 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8780 (pt0) REVERT: B 701 GLU cc_start: 0.9329 (tt0) cc_final: 0.8917 (pt0) REVERT: B 715 MET cc_start: 0.9154 (tmm) cc_final: 0.8884 (tmm) REVERT: B 900 GLU cc_start: 0.8835 (tp30) cc_final: 0.8427 (tm-30) REVERT: C 87 MET cc_start: 0.7731 (tmm) cc_final: 0.7235 (tmm) REVERT: C 253 CYS cc_start: 0.9133 (t) cc_final: 0.8890 (p) REVERT: C 309 ASN cc_start: 0.9404 (m-40) cc_final: 0.8701 (p0) REVERT: C 311 GLU cc_start: 0.8612 (tt0) cc_final: 0.7910 (tt0) REVERT: C 315 LYS cc_start: 0.8739 (tttt) cc_final: 0.8299 (pttp) REVERT: C 327 ASP cc_start: 0.9458 (t70) cc_final: 0.9245 (t0) REVERT: C 365 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8322 (ttm110) REVERT: C 436 MET cc_start: 0.9347 (mmm) cc_final: 0.9143 (mmm) REVERT: C 494 MET cc_start: 0.9120 (mmp) cc_final: 0.8187 (mtm) REVERT: C 510 CYS cc_start: 0.8644 (m) cc_final: 0.8170 (t) REVERT: C 533 MET cc_start: 0.9125 (tmm) cc_final: 0.8768 (tmm) REVERT: C 607 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8797 (t80) REVERT: C 633 ASP cc_start: 0.9084 (m-30) cc_final: 0.8641 (m-30) REVERT: C 649 MET cc_start: 0.9366 (tmm) cc_final: 0.9123 (ppp) REVERT: C 670 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8612 (p) REVERT: C 687 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8782 (pt0) REVERT: C 701 GLU cc_start: 0.9326 (tt0) cc_final: 0.8916 (pt0) REVERT: C 715 MET cc_start: 0.9153 (tmm) cc_final: 0.8884 (tmm) REVERT: C 900 GLU cc_start: 0.8841 (tp30) cc_final: 0.8430 (tm-30) REVERT: D 87 MET cc_start: 0.7731 (tmm) cc_final: 0.7236 (tmm) REVERT: D 253 CYS cc_start: 0.9130 (t) cc_final: 0.8890 (p) REVERT: D 309 ASN cc_start: 0.9404 (m-40) cc_final: 0.8702 (p0) REVERT: D 311 GLU cc_start: 0.8611 (tt0) cc_final: 0.7908 (tt0) REVERT: D 315 LYS cc_start: 0.8740 (tttt) cc_final: 0.8300 (pttp) REVERT: D 327 ASP cc_start: 0.9458 (t70) cc_final: 0.9245 (t0) REVERT: D 365 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8321 (ttm110) REVERT: D 436 MET cc_start: 0.9347 (mmm) cc_final: 0.9142 (mmm) REVERT: D 494 MET cc_start: 0.9121 (mmp) cc_final: 0.8186 (mtm) REVERT: D 510 CYS cc_start: 0.8644 (m) cc_final: 0.8169 (t) REVERT: D 533 MET cc_start: 0.9125 (tmm) cc_final: 0.8770 (tmm) REVERT: D 607 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8799 (t80) REVERT: D 633 ASP cc_start: 0.9083 (m-30) cc_final: 0.8638 (m-30) REVERT: D 649 MET cc_start: 0.9364 (tmm) cc_final: 0.9121 (ppp) REVERT: D 670 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8613 (p) REVERT: D 687 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8782 (pt0) REVERT: D 701 GLU cc_start: 0.9327 (tt0) cc_final: 0.8916 (pt0) REVERT: D 715 MET cc_start: 0.9155 (tmm) cc_final: 0.8887 (tmm) REVERT: D 900 GLU cc_start: 0.8835 (tp30) cc_final: 0.8394 (tm-30) outliers start: 66 outliers final: 24 residues processed: 414 average time/residue: 0.2859 time to fit residues: 191.0669 Evaluate side-chains 340 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 625 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 625 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 625 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 263 optimal weight: 1.9990 chunk 217 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 HIS A 460 ASN A 856 GLN ** B 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS B 460 ASN B 856 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 HIS C 460 ASN C 856 GLN ** D 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 HIS D 460 ASN D 856 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21848 Z= 0.334 Angle : 0.693 8.374 29520 Z= 0.356 Chirality : 0.042 0.192 3300 Planarity : 0.005 0.040 3712 Dihedral : 5.108 36.302 2900 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.51 % Favored : 93.34 % Rotamer: Outliers : 4.41 % Allowed : 21.66 % Favored : 73.93 % 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: 0.43 (0.16), residues: 2644 helix: 1.41 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -3.24 (0.18), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 750 HIS 0.006 0.001 HIS C 218 PHE 0.014 0.002 PHE A 731 TYR 0.016 0.002 TYR D 521 ARG 0.003 0.001 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 305 time to evaluate : 2.679 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 87 MET cc_start: 0.8059 (tmm) cc_final: 0.7619 (tmm) REVERT: A 295 MET cc_start: 0.9030 (tpp) cc_final: 0.8749 (tpp) REVERT: A 309 ASN cc_start: 0.9427 (t0) cc_final: 0.8668 (p0) REVERT: A 311 GLU cc_start: 0.8500 (tt0) cc_final: 0.7871 (tt0) REVERT: A 315 LYS cc_start: 0.8882 (tttt) cc_final: 0.8417 (pttp) REVERT: A 365 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8149 (ttm110) REVERT: A 403 MET cc_start: 0.8153 (tpp) cc_final: 0.7941 (tpp) REVERT: A 436 MET cc_start: 0.9476 (mmm) cc_final: 0.9211 (mmm) REVERT: A 496 MET cc_start: 0.9400 (mmt) cc_final: 0.9138 (mmm) REVERT: A 607 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8951 (t80) REVERT: A 633 ASP cc_start: 0.9044 (m-30) cc_final: 0.8743 (m-30) REVERT: A 649 MET cc_start: 0.9366 (tmm) cc_final: 0.9104 (ppp) REVERT: A 670 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 696 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.7842 (t0) REVERT: A 701 GLU cc_start: 0.9318 (tt0) cc_final: 0.8970 (pt0) REVERT: A 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8506 (tm-30) REVERT: B 87 MET cc_start: 0.8061 (tmm) cc_final: 0.7618 (tmm) REVERT: B 295 MET cc_start: 0.9029 (tpp) cc_final: 0.8749 (tpp) REVERT: B 309 ASN cc_start: 0.9427 (t0) cc_final: 0.8668 (p0) REVERT: B 311 GLU cc_start: 0.8499 (tt0) cc_final: 0.7869 (tt0) REVERT: B 315 LYS cc_start: 0.8881 (tttt) cc_final: 0.8417 (pttp) REVERT: B 365 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8148 (ttm110) REVERT: B 403 MET cc_start: 0.8154 (tpp) cc_final: 0.7943 (tpp) REVERT: B 436 MET cc_start: 0.9473 (mmm) cc_final: 0.9210 (mmm) REVERT: B 496 MET cc_start: 0.9401 (mmt) cc_final: 0.9138 (mmm) REVERT: B 607 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8949 (t80) REVERT: B 633 ASP cc_start: 0.9045 (m-30) cc_final: 0.8743 (m-30) REVERT: B 649 MET cc_start: 0.9366 (tmm) cc_final: 0.9104 (ppp) REVERT: B 670 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8532 (p) REVERT: B 696 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.7841 (t0) REVERT: B 701 GLU cc_start: 0.9318 (tt0) cc_final: 0.8970 (pt0) REVERT: B 900 GLU cc_start: 0.8872 (tp30) cc_final: 0.8507 (tm-30) REVERT: C 87 MET cc_start: 0.8060 (tmm) cc_final: 0.7617 (tmm) REVERT: C 295 MET cc_start: 0.9028 (tpp) cc_final: 0.8748 (tpp) REVERT: C 309 ASN cc_start: 0.9427 (t0) cc_final: 0.8668 (p0) REVERT: C 311 GLU cc_start: 0.8497 (tt0) cc_final: 0.7867 (tt0) REVERT: C 315 LYS cc_start: 0.8881 (tttt) cc_final: 0.8416 (pttp) REVERT: C 365 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8150 (ttm110) REVERT: C 403 MET cc_start: 0.8153 (tpp) cc_final: 0.7943 (tpp) REVERT: C 436 MET cc_start: 0.9474 (mmm) cc_final: 0.9210 (mmm) REVERT: C 496 MET cc_start: 0.9400 (mmt) cc_final: 0.9138 (mmm) REVERT: C 607 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8951 (t80) REVERT: C 633 ASP cc_start: 0.9043 (m-30) cc_final: 0.8743 (m-30) REVERT: C 649 MET cc_start: 0.9367 (tmm) cc_final: 0.9106 (ppp) REVERT: C 670 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 696 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.7841 (t0) REVERT: C 701 GLU cc_start: 0.9316 (tt0) cc_final: 0.8969 (pt0) REVERT: C 900 GLU cc_start: 0.8874 (tp30) cc_final: 0.8507 (tm-30) REVERT: D 87 MET cc_start: 0.8059 (tmm) cc_final: 0.7618 (tmm) REVERT: D 295 MET cc_start: 0.9029 (tpp) cc_final: 0.8748 (tpp) REVERT: D 309 ASN cc_start: 0.9426 (t0) cc_final: 0.8669 (p0) REVERT: D 311 GLU cc_start: 0.8497 (tt0) cc_final: 0.7866 (tt0) REVERT: D 315 LYS cc_start: 0.8882 (tttt) cc_final: 0.8418 (pttp) REVERT: D 365 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8150 (ttm110) REVERT: D 403 MET cc_start: 0.8154 (tpp) cc_final: 0.7941 (tpp) REVERT: D 436 MET cc_start: 0.9474 (mmm) cc_final: 0.9211 (mmm) REVERT: D 496 MET cc_start: 0.9400 (mmt) cc_final: 0.9137 (mmm) REVERT: D 607 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8951 (t80) REVERT: D 633 ASP cc_start: 0.9045 (m-30) cc_final: 0.8743 (m-30) REVERT: D 649 MET cc_start: 0.9366 (tmm) cc_final: 0.9104 (ppp) REVERT: D 670 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 696 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.7840 (t0) REVERT: D 701 GLU cc_start: 0.9318 (tt0) cc_final: 0.8970 (pt0) REVERT: D 900 GLU cc_start: 0.8841 (tp30) cc_final: 0.8461 (tm-30) outliers start: 99 outliers final: 47 residues processed: 364 average time/residue: 0.3044 time to fit residues: 176.8375 Evaluate side-chains 349 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 286 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 876 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 739 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 126 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 231 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 230 GLN C 230 GLN D 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21848 Z= 0.222 Angle : 0.600 7.445 29520 Z= 0.305 Chirality : 0.039 0.178 3300 Planarity : 0.004 0.040 3712 Dihedral : 4.706 36.870 2892 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.81 % Allowed : 23.89 % Favored : 73.31 % 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: 1.07 (0.17), residues: 2644 helix: 1.85 (0.12), residues: 2000 sheet: None (None), residues: 0 loop : -3.18 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 750 HIS 0.005 0.001 HIS D 218 PHE 0.013 0.001 PHE D 731 TYR 0.010 0.001 TYR B 658 ARG 0.001 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 317 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7950 (tmm) cc_final: 0.7531 (tmm) REVERT: A 150 GLU cc_start: 0.9426 (tp30) cc_final: 0.9208 (tm-30) REVERT: A 295 MET cc_start: 0.8932 (tpp) cc_final: 0.8659 (tpp) REVERT: A 309 ASN cc_start: 0.9456 (t0) cc_final: 0.8781 (p0) REVERT: A 311 GLU cc_start: 0.8461 (tt0) cc_final: 0.7879 (tt0) REVERT: A 315 LYS cc_start: 0.8826 (tttt) cc_final: 0.8471 (ptmm) REVERT: A 365 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8004 (ttm110) REVERT: A 436 MET cc_start: 0.9395 (mmm) cc_final: 0.9076 (mmm) REVERT: A 496 MET cc_start: 0.9389 (mmt) cc_final: 0.9137 (mmm) REVERT: A 607 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8970 (t80) REVERT: A 633 ASP cc_start: 0.9022 (m-30) cc_final: 0.8694 (m-30) REVERT: A 649 MET cc_start: 0.9371 (tmm) cc_final: 0.9062 (ppp) REVERT: A 670 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8532 (p) REVERT: A 696 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.7847 (t0) REVERT: A 701 GLU cc_start: 0.9292 (tt0) cc_final: 0.8975 (pt0) REVERT: A 710 VAL cc_start: 0.9551 (t) cc_final: 0.9261 (p) REVERT: A 900 GLU cc_start: 0.8850 (tp30) cc_final: 0.8453 (tm-30) REVERT: B 87 MET cc_start: 0.7948 (tmm) cc_final: 0.7531 (tmm) REVERT: B 150 GLU cc_start: 0.9427 (tp30) cc_final: 0.9208 (tm-30) REVERT: B 295 MET cc_start: 0.8931 (tpp) cc_final: 0.8659 (tpp) REVERT: B 309 ASN cc_start: 0.9456 (t0) cc_final: 0.8781 (p0) REVERT: B 311 GLU cc_start: 0.8460 (tt0) cc_final: 0.7878 (tt0) REVERT: B 315 LYS cc_start: 0.8825 (tttt) cc_final: 0.8471 (ptmm) REVERT: B 365 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8001 (ttm110) REVERT: B 436 MET cc_start: 0.9395 (mmm) cc_final: 0.9075 (mmm) REVERT: B 496 MET cc_start: 0.9388 (mmt) cc_final: 0.9137 (mmm) REVERT: B 607 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8968 (t80) REVERT: B 633 ASP cc_start: 0.9023 (m-30) cc_final: 0.8694 (m-30) REVERT: B 649 MET cc_start: 0.9372 (tmm) cc_final: 0.9063 (ppp) REVERT: B 670 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8531 (p) REVERT: B 696 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.7847 (t0) REVERT: B 701 GLU cc_start: 0.9292 (tt0) cc_final: 0.8975 (pt0) REVERT: B 710 VAL cc_start: 0.9550 (t) cc_final: 0.9261 (p) REVERT: B 900 GLU cc_start: 0.8843 (tp30) cc_final: 0.8449 (tm-30) REVERT: C 87 MET cc_start: 0.7951 (tmm) cc_final: 0.7534 (tmm) REVERT: C 150 GLU cc_start: 0.9427 (tp30) cc_final: 0.9209 (tm-30) REVERT: C 295 MET cc_start: 0.8931 (tpp) cc_final: 0.8659 (tpp) REVERT: C 309 ASN cc_start: 0.9456 (t0) cc_final: 0.8781 (p0) REVERT: C 311 GLU cc_start: 0.8458 (tt0) cc_final: 0.7879 (tt0) REVERT: C 315 LYS cc_start: 0.8825 (tttt) cc_final: 0.8471 (ptmm) REVERT: C 365 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8003 (ttm110) REVERT: C 436 MET cc_start: 0.9394 (mmm) cc_final: 0.9074 (mmm) REVERT: C 496 MET cc_start: 0.9388 (mmt) cc_final: 0.9136 (mmm) REVERT: C 607 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8970 (t80) REVERT: C 633 ASP cc_start: 0.9023 (m-30) cc_final: 0.8695 (m-30) REVERT: C 649 MET cc_start: 0.9373 (tmm) cc_final: 0.9063 (ppp) REVERT: C 670 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8531 (p) REVERT: C 696 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.7846 (t0) REVERT: C 701 GLU cc_start: 0.9292 (tt0) cc_final: 0.8974 (pt0) REVERT: C 710 VAL cc_start: 0.9550 (t) cc_final: 0.9261 (p) REVERT: C 900 GLU cc_start: 0.8848 (tp30) cc_final: 0.8453 (tm-30) REVERT: D 87 MET cc_start: 0.7951 (tmm) cc_final: 0.7534 (tmm) REVERT: D 150 GLU cc_start: 0.9426 (tp30) cc_final: 0.9208 (tm-30) REVERT: D 295 MET cc_start: 0.8932 (tpp) cc_final: 0.8661 (tpp) REVERT: D 309 ASN cc_start: 0.9456 (t0) cc_final: 0.8781 (p0) REVERT: D 311 GLU cc_start: 0.8458 (tt0) cc_final: 0.7877 (tt0) REVERT: D 315 LYS cc_start: 0.8826 (tttt) cc_final: 0.8471 (ptmm) REVERT: D 365 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8004 (ttm110) REVERT: D 436 MET cc_start: 0.9394 (mmm) cc_final: 0.9074 (mmm) REVERT: D 496 MET cc_start: 0.9388 (mmt) cc_final: 0.9137 (mmm) REVERT: D 607 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8969 (t80) REVERT: D 633 ASP cc_start: 0.9021 (m-30) cc_final: 0.8693 (m-30) REVERT: D 646 VAL cc_start: 0.9288 (t) cc_final: 0.9088 (p) REVERT: D 649 MET cc_start: 0.9372 (tmm) cc_final: 0.9063 (ppp) REVERT: D 670 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8532 (p) REVERT: D 696 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.7847 (t0) REVERT: D 701 GLU cc_start: 0.9292 (tt0) cc_final: 0.8975 (pt0) REVERT: D 710 VAL cc_start: 0.9550 (t) cc_final: 0.9261 (p) REVERT: D 900 GLU cc_start: 0.8832 (tp30) cc_final: 0.8425 (tm-30) outliers start: 63 outliers final: 31 residues processed: 364 average time/residue: 0.2936 time to fit residues: 170.3715 Evaluate side-chains 345 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 876 SER Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 760 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 21848 Z= 0.236 Angle : 0.611 7.326 29520 Z= 0.307 Chirality : 0.038 0.175 3300 Planarity : 0.004 0.041 3712 Dihedral : 4.618 35.147 2892 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.99 % Allowed : 22.10 % Favored : 72.91 % 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: 1.23 (0.17), residues: 2644 helix: 1.98 (0.12), residues: 2004 sheet: None (None), residues: 0 loop : -3.20 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 750 HIS 0.004 0.001 HIS A 218 PHE 0.011 0.001 PHE A 731 TYR 0.009 0.001 TYR A 285 ARG 0.002 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 313 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7924 (tmm) cc_final: 0.7444 (tmm) REVERT: A 150 GLU cc_start: 0.9424 (tp30) cc_final: 0.9141 (tm-30) REVERT: A 186 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8379 (t80) REVERT: A 295 MET cc_start: 0.8974 (tpp) cc_final: 0.8660 (tpp) REVERT: A 309 ASN cc_start: 0.9420 (t0) cc_final: 0.8735 (p0) REVERT: A 311 GLU cc_start: 0.8461 (tt0) cc_final: 0.7881 (tt0) REVERT: A 315 LYS cc_start: 0.8844 (tttt) cc_final: 0.8538 (ptmm) REVERT: A 365 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: A 436 MET cc_start: 0.9395 (mmm) cc_final: 0.9036 (mmm) REVERT: A 496 MET cc_start: 0.9374 (mmt) cc_final: 0.9127 (mmm) REVERT: A 607 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8950 (t80) REVERT: A 633 ASP cc_start: 0.9018 (m-30) cc_final: 0.8718 (m-30) REVERT: A 649 MET cc_start: 0.9350 (tmm) cc_final: 0.8993 (ppp) REVERT: A 670 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 696 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.7836 (t0) REVERT: A 701 GLU cc_start: 0.9310 (tt0) cc_final: 0.9014 (pt0) REVERT: A 710 VAL cc_start: 0.9550 (OUTLIER) cc_final: 0.9265 (p) REVERT: A 900 GLU cc_start: 0.8859 (tp30) cc_final: 0.8476 (tm-30) REVERT: B 87 MET cc_start: 0.7924 (tmm) cc_final: 0.7440 (tmm) REVERT: B 150 GLU cc_start: 0.9423 (tp30) cc_final: 0.9140 (tm-30) REVERT: B 186 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 295 MET cc_start: 0.8972 (tpp) cc_final: 0.8660 (tpp) REVERT: B 309 ASN cc_start: 0.9420 (t0) cc_final: 0.8736 (p0) REVERT: B 311 GLU cc_start: 0.8459 (tt0) cc_final: 0.7879 (tt0) REVERT: B 315 LYS cc_start: 0.8842 (tttt) cc_final: 0.8539 (ptmm) REVERT: B 365 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8192 (ttm110) REVERT: B 436 MET cc_start: 0.9394 (mmm) cc_final: 0.9036 (mmm) REVERT: B 496 MET cc_start: 0.9374 (mmt) cc_final: 0.9126 (mmm) REVERT: B 607 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8950 (t80) REVERT: B 633 ASP cc_start: 0.9019 (m-30) cc_final: 0.8719 (m-30) REVERT: B 649 MET cc_start: 0.9352 (tmm) cc_final: 0.8995 (ppp) REVERT: B 670 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8602 (p) REVERT: B 696 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.7835 (t0) REVERT: B 701 GLU cc_start: 0.9308 (tt0) cc_final: 0.9012 (pt0) REVERT: B 710 VAL cc_start: 0.9550 (OUTLIER) cc_final: 0.9265 (p) REVERT: B 900 GLU cc_start: 0.8851 (tp30) cc_final: 0.8464 (tm-30) REVERT: C 87 MET cc_start: 0.7923 (tmm) cc_final: 0.7440 (tmm) REVERT: C 150 GLU cc_start: 0.9425 (tp30) cc_final: 0.9142 (tm-30) REVERT: C 186 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8379 (t80) REVERT: C 295 MET cc_start: 0.8973 (tpp) cc_final: 0.8660 (tpp) REVERT: C 309 ASN cc_start: 0.9421 (t0) cc_final: 0.8736 (p0) REVERT: C 311 GLU cc_start: 0.8461 (tt0) cc_final: 0.7879 (tt0) REVERT: C 315 LYS cc_start: 0.8843 (tttt) cc_final: 0.8537 (ptmm) REVERT: C 365 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8193 (ttm110) REVERT: C 436 MET cc_start: 0.9393 (mmm) cc_final: 0.9034 (mmm) REVERT: C 496 MET cc_start: 0.9375 (mmt) cc_final: 0.9126 (mmm) REVERT: C 607 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8956 (t80) REVERT: C 633 ASP cc_start: 0.9018 (m-30) cc_final: 0.8719 (m-30) REVERT: C 649 MET cc_start: 0.9350 (tmm) cc_final: 0.8994 (ppp) REVERT: C 670 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8602 (p) REVERT: C 696 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.7835 (t0) REVERT: C 701 GLU cc_start: 0.9308 (tt0) cc_final: 0.9013 (pt0) REVERT: C 710 VAL cc_start: 0.9550 (OUTLIER) cc_final: 0.9264 (p) REVERT: C 900 GLU cc_start: 0.8855 (tp30) cc_final: 0.8468 (tm-30) REVERT: D 87 MET cc_start: 0.7920 (tmm) cc_final: 0.7441 (tmm) REVERT: D 150 GLU cc_start: 0.9424 (tp30) cc_final: 0.9140 (tm-30) REVERT: D 186 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8380 (t80) REVERT: D 295 MET cc_start: 0.8973 (tpp) cc_final: 0.8661 (tpp) REVERT: D 309 ASN cc_start: 0.9421 (t0) cc_final: 0.8736 (p0) REVERT: D 311 GLU cc_start: 0.8462 (tt0) cc_final: 0.7880 (tt0) REVERT: D 315 LYS cc_start: 0.8844 (tttt) cc_final: 0.8538 (ptmm) REVERT: D 365 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8194 (ttm110) REVERT: D 436 MET cc_start: 0.9393 (mmm) cc_final: 0.9036 (mmm) REVERT: D 496 MET cc_start: 0.9374 (mmt) cc_final: 0.9126 (mmm) REVERT: D 607 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8951 (t80) REVERT: D 633 ASP cc_start: 0.9018 (m-30) cc_final: 0.8717 (m-30) REVERT: D 649 MET cc_start: 0.9368 (tmm) cc_final: 0.9014 (ppp) REVERT: D 670 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8603 (p) REVERT: D 696 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.7835 (t0) REVERT: D 701 GLU cc_start: 0.9310 (tt0) cc_final: 0.9013 (pt0) REVERT: D 710 VAL cc_start: 0.9550 (OUTLIER) cc_final: 0.9264 (p) REVERT: D 900 GLU cc_start: 0.8878 (tp30) cc_final: 0.8499 (tm-30) outliers start: 112 outliers final: 64 residues processed: 401 average time/residue: 0.2868 time to fit residues: 187.7410 Evaluate side-chains 383 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 295 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 131 TYR Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 TYR Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 131 TYR Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 876 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 608 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 760 LEU Chi-restraints excluded: chain D residue 876 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 21848 Z= 0.301 Angle : 0.640 7.250 29520 Z= 0.329 Chirality : 0.039 0.183 3300 Planarity : 0.004 0.043 3712 Dihedral : 4.743 32.745 2892 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.84 % Allowed : 23.44 % Favored : 70.72 % 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: 1.16 (0.17), residues: 2644 helix: 1.91 (0.12), residues: 2012 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 391 HIS 0.004 0.001 HIS D 218 PHE 0.014 0.001 PHE D 541 TYR 0.010 0.001 TYR D 285 ARG 0.003 0.000 ARG C 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 308 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8048 (tmm) cc_final: 0.7601 (tmm) REVERT: A 150 GLU cc_start: 0.9432 (tp30) cc_final: 0.9153 (tm-30) REVERT: A 295 MET cc_start: 0.9030 (tpp) cc_final: 0.8682 (tpp) REVERT: A 309 ASN cc_start: 0.9460 (t0) cc_final: 0.8796 (p0) REVERT: A 311 GLU cc_start: 0.8510 (tt0) cc_final: 0.7928 (tt0) REVERT: A 315 LYS cc_start: 0.8905 (tttt) cc_final: 0.8576 (ptmm) REVERT: A 365 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8299 (ttm110) REVERT: A 419 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: A 496 MET cc_start: 0.9392 (mmt) cc_final: 0.9119 (mmm) REVERT: A 607 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9086 (t80) REVERT: A 633 ASP cc_start: 0.9050 (m-30) cc_final: 0.8784 (m-30) REVERT: A 649 MET cc_start: 0.9356 (tmm) cc_final: 0.9000 (ppp) REVERT: A 670 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 696 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7905 (t0) REVERT: A 701 GLU cc_start: 0.9328 (tt0) cc_final: 0.9035 (pt0) REVERT: A 710 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9245 (p) REVERT: A 715 MET cc_start: 0.9023 (tmm) cc_final: 0.8789 (tmm) REVERT: A 900 GLU cc_start: 0.8868 (tp30) cc_final: 0.8476 (tm-30) REVERT: B 87 MET cc_start: 0.8043 (tmm) cc_final: 0.7601 (tmm) REVERT: B 150 GLU cc_start: 0.9432 (tp30) cc_final: 0.9152 (tm-30) REVERT: B 295 MET cc_start: 0.9029 (tpp) cc_final: 0.8680 (tpp) REVERT: B 309 ASN cc_start: 0.9460 (t0) cc_final: 0.8797 (p0) REVERT: B 311 GLU cc_start: 0.8509 (tt0) cc_final: 0.7929 (tt0) REVERT: B 315 LYS cc_start: 0.8904 (tttt) cc_final: 0.8577 (ptmm) REVERT: B 365 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8300 (ttm110) REVERT: B 419 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: B 496 MET cc_start: 0.9394 (mmt) cc_final: 0.9120 (mmm) REVERT: B 607 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.9083 (t80) REVERT: B 633 ASP cc_start: 0.9051 (m-30) cc_final: 0.8784 (m-30) REVERT: B 649 MET cc_start: 0.9355 (tmm) cc_final: 0.9001 (ppp) REVERT: B 670 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8622 (p) REVERT: B 696 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.7905 (t0) REVERT: B 701 GLU cc_start: 0.9325 (tt0) cc_final: 0.9032 (pt0) REVERT: B 710 VAL cc_start: 0.9561 (OUTLIER) cc_final: 0.9247 (p) REVERT: B 715 MET cc_start: 0.9026 (tmm) cc_final: 0.8791 (tmm) REVERT: B 900 GLU cc_start: 0.8865 (tp30) cc_final: 0.8471 (tm-30) REVERT: C 87 MET cc_start: 0.8047 (tmm) cc_final: 0.7603 (tmm) REVERT: C 150 GLU cc_start: 0.9434 (tp30) cc_final: 0.9154 (tm-30) REVERT: C 295 MET cc_start: 0.9030 (tpp) cc_final: 0.8680 (tpp) REVERT: C 309 ASN cc_start: 0.9461 (t0) cc_final: 0.8798 (p0) REVERT: C 311 GLU cc_start: 0.8507 (tt0) cc_final: 0.7927 (tt0) REVERT: C 315 LYS cc_start: 0.8902 (tttt) cc_final: 0.8575 (ptmm) REVERT: C 365 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8303 (ttm110) REVERT: C 419 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: C 496 MET cc_start: 0.9393 (mmt) cc_final: 0.9119 (mmm) REVERT: C 607 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.9081 (t80) REVERT: C 633 ASP cc_start: 0.9049 (m-30) cc_final: 0.8782 (m-30) REVERT: C 649 MET cc_start: 0.9355 (tmm) cc_final: 0.8999 (ppp) REVERT: C 670 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8621 (p) REVERT: C 696 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.7904 (t0) REVERT: C 701 GLU cc_start: 0.9324 (tt0) cc_final: 0.9032 (pt0) REVERT: C 710 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9246 (p) REVERT: C 715 MET cc_start: 0.9025 (tmm) cc_final: 0.8791 (tmm) REVERT: C 900 GLU cc_start: 0.8866 (tp30) cc_final: 0.8470 (tm-30) REVERT: D 87 MET cc_start: 0.8045 (tmm) cc_final: 0.7603 (tmm) REVERT: D 150 GLU cc_start: 0.9431 (tp30) cc_final: 0.9152 (tm-30) REVERT: D 295 MET cc_start: 0.9031 (tpp) cc_final: 0.8682 (tpp) REVERT: D 309 ASN cc_start: 0.9461 (t0) cc_final: 0.8797 (p0) REVERT: D 311 GLU cc_start: 0.8507 (tt0) cc_final: 0.7926 (tt0) REVERT: D 315 LYS cc_start: 0.8904 (tttt) cc_final: 0.8576 (ptmm) REVERT: D 365 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8302 (ttm110) REVERT: D 419 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: D 496 MET cc_start: 0.9392 (mmt) cc_final: 0.9118 (mmm) REVERT: D 607 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.9084 (t80) REVERT: D 633 ASP cc_start: 0.9044 (m-30) cc_final: 0.8774 (m-30) REVERT: D 649 MET cc_start: 0.9337 (tmm) cc_final: 0.8994 (ppp) REVERT: D 670 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 696 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.7905 (t0) REVERT: D 701 GLU cc_start: 0.9326 (tt0) cc_final: 0.9033 (pt0) REVERT: D 710 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9246 (p) REVERT: D 715 MET cc_start: 0.9023 (tmm) cc_final: 0.8790 (tmm) REVERT: D 900 GLU cc_start: 0.8885 (tp30) cc_final: 0.8499 (tm-30) outliers start: 131 outliers final: 71 residues processed: 411 average time/residue: 0.2880 time to fit residues: 192.7130 Evaluate side-chains 389 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 294 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 876 SER Chi-restraints excluded: chain B residue 88 PHE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 419 PHE Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 739 ASP Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain B residue 876 SER Chi-restraints excluded: chain C residue 88 PHE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 365 ARG Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 419 PHE Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain C residue 876 SER Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 365 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 608 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 677 THR Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 710 VAL Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 760 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 144 optimal weight: 0.0570 chunk 258 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 732 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21848 Z= 0.160 Angle : 0.591 10.072 29520 Z= 0.291 Chirality : 0.037 0.200 3300 Planarity : 0.004 0.042 3712 Dihedral : 4.255 21.220 2884 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.61 % Allowed : 24.73 % Favored : 71.66 % 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: 1.54 (0.17), residues: 2644 helix: 2.19 (0.12), residues: 2016 sheet: None (None), residues: 0 loop : -3.16 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 750 HIS 0.005 0.001 HIS D 218 PHE 0.010 0.001 PHE B 407 TYR 0.009 0.001 TYR A 131 ARG 0.002 0.000 ARG B 853 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 331 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8039 (tmm) cc_final: 0.7621 (tmm) REVERT: A 150 GLU cc_start: 0.9409 (tp30) cc_final: 0.9160 (tm-30) REVERT: A 186 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8386 (t80) REVERT: A 295 MET cc_start: 0.8961 (tpp) cc_final: 0.8640 (tpp) REVERT: A 309 ASN cc_start: 0.9372 (t0) cc_final: 0.8777 (p0) REVERT: A 310 ILE cc_start: 0.8464 (mm) cc_final: 0.8258 (tt) REVERT: A 311 GLU cc_start: 0.8303 (tt0) cc_final: 0.7680 (tt0) REVERT: A 436 MET cc_start: 0.9437 (mmm) cc_final: 0.9070 (mmm) REVERT: A 496 MET cc_start: 0.9330 (mmt) cc_final: 0.9082 (mmm) REVERT: A 607 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8605 (t80) REVERT: A 633 ASP cc_start: 0.9031 (m-30) cc_final: 0.8708 (m-30) REVERT: A 649 MET cc_start: 0.9308 (tmm) cc_final: 0.8934 (ppp) REVERT: A 670 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8521 (p) REVERT: A 701 GLU cc_start: 0.9294 (tt0) cc_final: 0.8810 (pt0) REVERT: A 710 VAL cc_start: 0.9520 (t) cc_final: 0.9268 (p) REVERT: A 900 GLU cc_start: 0.8886 (tp30) cc_final: 0.8490 (tm-30) REVERT: B 87 MET cc_start: 0.8038 (tmm) cc_final: 0.7621 (tmm) REVERT: B 150 GLU cc_start: 0.9408 (tp30) cc_final: 0.9160 (tm-30) REVERT: B 186 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8389 (t80) REVERT: B 295 MET cc_start: 0.8962 (tpp) cc_final: 0.8638 (tpp) REVERT: B 309 ASN cc_start: 0.9372 (t0) cc_final: 0.8776 (p0) REVERT: B 310 ILE cc_start: 0.8464 (mm) cc_final: 0.8257 (tt) REVERT: B 311 GLU cc_start: 0.8306 (tt0) cc_final: 0.7684 (tt0) REVERT: B 436 MET cc_start: 0.9436 (mmm) cc_final: 0.9070 (mmm) REVERT: B 496 MET cc_start: 0.9330 (mmt) cc_final: 0.9083 (mmm) REVERT: B 607 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8604 (t80) REVERT: B 633 ASP cc_start: 0.9033 (m-30) cc_final: 0.8709 (m-30) REVERT: B 649 MET cc_start: 0.9307 (tmm) cc_final: 0.8935 (ppp) REVERT: B 670 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8522 (p) REVERT: B 701 GLU cc_start: 0.9293 (tt0) cc_final: 0.8808 (pt0) REVERT: B 710 VAL cc_start: 0.9520 (t) cc_final: 0.9267 (p) REVERT: B 900 GLU cc_start: 0.8883 (tp30) cc_final: 0.8476 (tm-30) REVERT: C 87 MET cc_start: 0.8035 (tmm) cc_final: 0.7620 (tmm) REVERT: C 150 GLU cc_start: 0.9411 (tp30) cc_final: 0.9162 (tm-30) REVERT: C 186 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8388 (t80) REVERT: C 295 MET cc_start: 0.8962 (tpp) cc_final: 0.8640 (tpp) REVERT: C 309 ASN cc_start: 0.9373 (t0) cc_final: 0.8778 (p0) REVERT: C 310 ILE cc_start: 0.8469 (mm) cc_final: 0.8261 (tt) REVERT: C 311 GLU cc_start: 0.8304 (tt0) cc_final: 0.7681 (tt0) REVERT: C 436 MET cc_start: 0.9436 (mmm) cc_final: 0.9069 (mmm) REVERT: C 496 MET cc_start: 0.9330 (mmt) cc_final: 0.9084 (mmm) REVERT: C 607 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8628 (t80) REVERT: C 633 ASP cc_start: 0.9032 (m-30) cc_final: 0.8708 (m-30) REVERT: C 649 MET cc_start: 0.9309 (tmm) cc_final: 0.8936 (ppp) REVERT: C 670 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 701 GLU cc_start: 0.9295 (tt0) cc_final: 0.8810 (pt0) REVERT: C 710 VAL cc_start: 0.9519 (t) cc_final: 0.9267 (p) REVERT: C 900 GLU cc_start: 0.8883 (tp30) cc_final: 0.8473 (tm-30) REVERT: D 87 MET cc_start: 0.8039 (tmm) cc_final: 0.7620 (tmm) REVERT: D 150 GLU cc_start: 0.9409 (tp30) cc_final: 0.9159 (tm-30) REVERT: D 186 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8386 (t80) REVERT: D 295 MET cc_start: 0.8963 (tpp) cc_final: 0.8641 (tpp) REVERT: D 309 ASN cc_start: 0.9373 (t0) cc_final: 0.8777 (p0) REVERT: D 310 ILE cc_start: 0.8463 (mm) cc_final: 0.8257 (tt) REVERT: D 311 GLU cc_start: 0.8303 (tt0) cc_final: 0.7679 (tt0) REVERT: D 436 MET cc_start: 0.9437 (mmm) cc_final: 0.9070 (mmm) REVERT: D 496 MET cc_start: 0.9329 (mmt) cc_final: 0.9082 (mmm) REVERT: D 607 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8603 (t80) REVERT: D 633 ASP cc_start: 0.9030 (m-30) cc_final: 0.8705 (m-30) REVERT: D 649 MET cc_start: 0.9307 (tmm) cc_final: 0.8944 (ppp) REVERT: D 670 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8521 (p) REVERT: D 701 GLU cc_start: 0.9294 (tt0) cc_final: 0.8809 (pt0) REVERT: D 710 VAL cc_start: 0.9520 (t) cc_final: 0.9268 (p) REVERT: D 900 GLU cc_start: 0.8878 (tp30) cc_final: 0.8521 (tm-30) outliers start: 81 outliers final: 44 residues processed: 400 average time/residue: 0.2798 time to fit residues: 182.2256 Evaluate side-chains 334 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 278 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 760 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 608 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 760 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 7.9990 chunk 103 optimal weight: 0.0970 chunk 154 optimal weight: 2.9990 chunk 77 optimal weight: 0.0040 chunk 50 optimal weight: 0.0870 chunk 164 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 732 GLN C 732 GLN D 732 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21848 Z= 0.153 Angle : 0.589 8.606 29520 Z= 0.289 Chirality : 0.038 0.193 3300 Planarity : 0.004 0.042 3712 Dihedral : 4.064 20.265 2884 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.76 % Allowed : 26.25 % Favored : 70.99 % 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: 1.61 (0.17), residues: 2644 helix: 2.25 (0.12), residues: 2008 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 391 HIS 0.005 0.001 HIS D 218 PHE 0.010 0.001 PHE B 407 TYR 0.009 0.001 TYR A 131 ARG 0.001 0.000 ARG D 853 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 304 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7790 (tmm) cc_final: 0.7392 (tmm) REVERT: A 186 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 206 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8705 (t80) REVERT: A 295 MET cc_start: 0.8919 (tpp) cc_final: 0.8627 (tpp) REVERT: A 309 ASN cc_start: 0.9150 (t0) cc_final: 0.8775 (p0) REVERT: A 311 GLU cc_start: 0.8228 (tt0) cc_final: 0.7542 (tt0) REVERT: A 368 LEU cc_start: 0.9645 (tp) cc_final: 0.9441 (tt) REVERT: A 496 MET cc_start: 0.9315 (mmt) cc_final: 0.8993 (mmm) REVERT: A 505 MET cc_start: 0.9108 (mtt) cc_final: 0.8632 (mmm) REVERT: A 633 ASP cc_start: 0.9095 (m-30) cc_final: 0.8834 (m-30) REVERT: A 649 MET cc_start: 0.9276 (tmm) cc_final: 0.8878 (ppp) REVERT: A 670 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 701 GLU cc_start: 0.9260 (tt0) cc_final: 0.8802 (pt0) REVERT: A 710 VAL cc_start: 0.9435 (t) cc_final: 0.9170 (p) REVERT: A 859 MET cc_start: 0.9411 (mmp) cc_final: 0.8981 (mmm) REVERT: A 900 GLU cc_start: 0.8882 (tp30) cc_final: 0.8371 (tm-30) REVERT: B 87 MET cc_start: 0.7788 (tmm) cc_final: 0.7393 (tmm) REVERT: B 186 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8492 (t80) REVERT: B 206 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8702 (t80) REVERT: B 295 MET cc_start: 0.8920 (tpp) cc_final: 0.8625 (tpp) REVERT: B 309 ASN cc_start: 0.9151 (t0) cc_final: 0.8774 (p0) REVERT: B 311 GLU cc_start: 0.8234 (tt0) cc_final: 0.7549 (tt0) REVERT: B 368 LEU cc_start: 0.9644 (tp) cc_final: 0.9441 (tt) REVERT: B 496 MET cc_start: 0.9315 (mmt) cc_final: 0.8992 (mmm) REVERT: B 505 MET cc_start: 0.9109 (mtt) cc_final: 0.8630 (mmm) REVERT: B 633 ASP cc_start: 0.9096 (m-30) cc_final: 0.8835 (m-30) REVERT: B 649 MET cc_start: 0.9275 (tmm) cc_final: 0.8877 (ppp) REVERT: B 670 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8561 (p) REVERT: B 701 GLU cc_start: 0.9257 (tt0) cc_final: 0.8799 (pt0) REVERT: B 710 VAL cc_start: 0.9435 (t) cc_final: 0.9170 (p) REVERT: B 859 MET cc_start: 0.9411 (mmp) cc_final: 0.8981 (mmm) REVERT: B 900 GLU cc_start: 0.8912 (tp30) cc_final: 0.8563 (tm-30) REVERT: C 87 MET cc_start: 0.7791 (tmm) cc_final: 0.7395 (tmm) REVERT: C 186 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8491 (t80) REVERT: C 206 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8704 (t80) REVERT: C 295 MET cc_start: 0.8921 (tpp) cc_final: 0.8626 (tpp) REVERT: C 309 ASN cc_start: 0.9152 (t0) cc_final: 0.8776 (p0) REVERT: C 311 GLU cc_start: 0.8232 (tt0) cc_final: 0.7547 (tt0) REVERT: C 368 LEU cc_start: 0.9644 (tp) cc_final: 0.9441 (tt) REVERT: C 496 MET cc_start: 0.9324 (mmt) cc_final: 0.9001 (mmm) REVERT: C 505 MET cc_start: 0.9109 (mtt) cc_final: 0.8633 (mmm) REVERT: C 633 ASP cc_start: 0.9097 (m-30) cc_final: 0.8836 (m-30) REVERT: C 649 MET cc_start: 0.9278 (tmm) cc_final: 0.8879 (ppp) REVERT: C 670 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8561 (p) REVERT: C 701 GLU cc_start: 0.9257 (tt0) cc_final: 0.8798 (pt0) REVERT: C 710 VAL cc_start: 0.9435 (t) cc_final: 0.9170 (p) REVERT: C 859 MET cc_start: 0.9412 (mmp) cc_final: 0.8982 (mmm) REVERT: C 900 GLU cc_start: 0.8887 (tp30) cc_final: 0.8546 (tm-30) REVERT: D 87 MET cc_start: 0.7790 (tmm) cc_final: 0.7392 (tmm) REVERT: D 186 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8490 (t80) REVERT: D 206 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8705 (t80) REVERT: D 295 MET cc_start: 0.8922 (tpp) cc_final: 0.8627 (tpp) REVERT: D 309 ASN cc_start: 0.9152 (t0) cc_final: 0.8775 (p0) REVERT: D 311 GLU cc_start: 0.8231 (tt0) cc_final: 0.7541 (tt0) REVERT: D 368 LEU cc_start: 0.9645 (tp) cc_final: 0.9441 (tt) REVERT: D 496 MET cc_start: 0.9314 (mmt) cc_final: 0.8991 (mmm) REVERT: D 505 MET cc_start: 0.9108 (mtt) cc_final: 0.8632 (mmm) REVERT: D 633 ASP cc_start: 0.9096 (m-30) cc_final: 0.8833 (m-30) REVERT: D 649 MET cc_start: 0.9272 (tmm) cc_final: 0.8871 (ppp) REVERT: D 670 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8554 (p) REVERT: D 701 GLU cc_start: 0.9258 (tt0) cc_final: 0.8801 (pt0) REVERT: D 710 VAL cc_start: 0.9506 (t) cc_final: 0.9244 (p) REVERT: D 859 MET cc_start: 0.9412 (mmp) cc_final: 0.8983 (mmm) REVERT: D 900 GLU cc_start: 0.8882 (tp30) cc_final: 0.8415 (tm-30) outliers start: 62 outliers final: 28 residues processed: 354 average time/residue: 0.2751 time to fit residues: 160.9001 Evaluate side-chains 316 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 206 PHE Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 9.9990 chunk 225 optimal weight: 0.2980 chunk 240 optimal weight: 10.0000 chunk 144 optimal weight: 0.4980 chunk 104 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 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 249 HIS B 249 HIS C 249 HIS D 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21848 Z= 0.233 Angle : 0.648 10.860 29520 Z= 0.316 Chirality : 0.041 0.298 3300 Planarity : 0.004 0.042 3712 Dihedral : 4.157 21.407 2884 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.34 % Allowed : 25.53 % Favored : 71.12 % 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: 1.56 (0.17), residues: 2644 helix: 2.18 (0.12), residues: 2012 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 391 HIS 0.004 0.001 HIS B 218 PHE 0.017 0.001 PHE D 607 TYR 0.010 0.001 TYR C 521 ARG 0.001 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 277 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7875 (tmm) cc_final: 0.7484 (tmm) REVERT: A 186 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8419 (t80) REVERT: A 295 MET cc_start: 0.9056 (tpp) cc_final: 0.8772 (tpp) REVERT: A 309 ASN cc_start: 0.9114 (t0) cc_final: 0.8694 (p0) REVERT: A 311 GLU cc_start: 0.8722 (tt0) cc_final: 0.8104 (tt0) REVERT: A 496 MET cc_start: 0.9359 (mmt) cc_final: 0.9111 (mmm) REVERT: A 505 MET cc_start: 0.9059 (mtt) cc_final: 0.8616 (mmm) REVERT: A 633 ASP cc_start: 0.9041 (m-30) cc_final: 0.8769 (m-30) REVERT: A 649 MET cc_start: 0.9299 (tmm) cc_final: 0.8915 (ppp) REVERT: A 670 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8642 (p) REVERT: A 696 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.7464 (t0) REVERT: A 701 GLU cc_start: 0.9272 (tt0) cc_final: 0.8777 (pt0) REVERT: A 710 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9191 (p) REVERT: A 900 GLU cc_start: 0.8889 (tp30) cc_final: 0.8404 (tm-30) REVERT: B 87 MET cc_start: 0.7872 (tmm) cc_final: 0.7484 (tmm) REVERT: B 186 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8417 (t80) REVERT: B 295 MET cc_start: 0.9056 (tpp) cc_final: 0.8772 (tpp) REVERT: B 309 ASN cc_start: 0.9115 (t0) cc_final: 0.8695 (p0) REVERT: B 311 GLU cc_start: 0.8723 (tt0) cc_final: 0.8105 (tt0) REVERT: B 496 MET cc_start: 0.9358 (mmt) cc_final: 0.9110 (mmm) REVERT: B 505 MET cc_start: 0.9060 (mtt) cc_final: 0.8619 (mmm) REVERT: B 633 ASP cc_start: 0.9041 (m-30) cc_final: 0.8769 (m-30) REVERT: B 649 MET cc_start: 0.9298 (tmm) cc_final: 0.8916 (ppp) REVERT: B 670 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8641 (p) REVERT: B 696 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.7466 (t0) REVERT: B 701 GLU cc_start: 0.9271 (tt0) cc_final: 0.8777 (pt0) REVERT: B 710 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9191 (p) REVERT: B 900 GLU cc_start: 0.8914 (tp30) cc_final: 0.8439 (tm-30) REVERT: C 87 MET cc_start: 0.7869 (tmm) cc_final: 0.7483 (tmm) REVERT: C 186 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8417 (t80) REVERT: C 295 MET cc_start: 0.9058 (tpp) cc_final: 0.8774 (tpp) REVERT: C 309 ASN cc_start: 0.9114 (t0) cc_final: 0.8695 (p0) REVERT: C 311 GLU cc_start: 0.8722 (tt0) cc_final: 0.8105 (tt0) REVERT: C 496 MET cc_start: 0.9357 (mmt) cc_final: 0.9110 (mmm) REVERT: C 505 MET cc_start: 0.9058 (mtt) cc_final: 0.8616 (mmm) REVERT: C 633 ASP cc_start: 0.9041 (m-30) cc_final: 0.8769 (m-30) REVERT: C 649 MET cc_start: 0.9299 (tmm) cc_final: 0.8916 (ppp) REVERT: C 670 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8641 (p) REVERT: C 696 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.7465 (t0) REVERT: C 701 GLU cc_start: 0.9270 (tt0) cc_final: 0.8776 (pt0) REVERT: C 710 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9190 (p) REVERT: C 900 GLU cc_start: 0.8879 (tp30) cc_final: 0.8424 (tm-30) REVERT: D 87 MET cc_start: 0.7862 (tmm) cc_final: 0.7452 (tmm) REVERT: D 186 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8418 (t80) REVERT: D 295 MET cc_start: 0.9056 (tpp) cc_final: 0.8772 (tpp) REVERT: D 309 ASN cc_start: 0.9115 (t0) cc_final: 0.8695 (p0) REVERT: D 311 GLU cc_start: 0.8723 (tt0) cc_final: 0.8104 (tt0) REVERT: D 496 MET cc_start: 0.9357 (mmt) cc_final: 0.9109 (mmm) REVERT: D 505 MET cc_start: 0.9060 (mtt) cc_final: 0.8620 (mmm) REVERT: D 633 ASP cc_start: 0.9041 (m-30) cc_final: 0.8768 (m-30) REVERT: D 649 MET cc_start: 0.9296 (tmm) cc_final: 0.8915 (ppp) REVERT: D 670 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8638 (p) REVERT: D 696 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.7463 (t0) REVERT: D 701 GLU cc_start: 0.9272 (tt0) cc_final: 0.8777 (pt0) REVERT: D 710 VAL cc_start: 0.9462 (OUTLIER) cc_final: 0.9192 (p) REVERT: D 900 GLU cc_start: 0.8920 (tp30) cc_final: 0.8457 (tm-30) outliers start: 75 outliers final: 50 residues processed: 344 average time/residue: 0.2853 time to fit residues: 165.5384 Evaluate side-chains 338 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 272 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 521 TYR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 521 TYR Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 249 HIS C 249 HIS D 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21848 Z= 0.248 Angle : 0.674 11.321 29520 Z= 0.329 Chirality : 0.041 0.325 3300 Planarity : 0.004 0.041 3712 Dihedral : 4.247 22.538 2884 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.99 % Allowed : 26.60 % Favored : 70.41 % 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: 1.47 (0.17), residues: 2644 helix: 2.12 (0.12), residues: 2004 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 391 HIS 0.004 0.001 HIS D 218 PHE 0.020 0.001 PHE C 607 TYR 0.009 0.001 TYR C 285 ARG 0.002 0.000 ARG D 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5288 Ramachandran restraints generated. 2644 Oldfield, 0 Emsley, 2644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 277 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8045 (tmm) cc_final: 0.7670 (tmm) REVERT: A 186 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8298 (t80) REVERT: A 295 MET cc_start: 0.9081 (tpp) cc_final: 0.8763 (tpp) REVERT: A 309 ASN cc_start: 0.9160 (t0) cc_final: 0.8745 (p0) REVERT: A 311 GLU cc_start: 0.8741 (tt0) cc_final: 0.8114 (tt0) REVERT: A 436 MET cc_start: 0.9440 (mmm) cc_final: 0.9046 (mmm) REVERT: A 496 MET cc_start: 0.9380 (mmt) cc_final: 0.9041 (mmm) REVERT: A 505 MET cc_start: 0.9052 (mtt) cc_final: 0.8620 (mmm) REVERT: A 633 ASP cc_start: 0.9022 (m-30) cc_final: 0.8739 (m-30) REVERT: A 649 MET cc_start: 0.9320 (tmm) cc_final: 0.9052 (ppp) REVERT: A 670 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 696 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.7514 (t0) REVERT: A 701 GLU cc_start: 0.9284 (tt0) cc_final: 0.8788 (pt0) REVERT: A 710 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9250 (p) REVERT: A 859 MET cc_start: 0.9441 (mmp) cc_final: 0.8954 (mmm) REVERT: A 900 GLU cc_start: 0.8879 (tp30) cc_final: 0.8382 (tm-30) REVERT: B 87 MET cc_start: 0.8044 (tmm) cc_final: 0.7669 (tmm) REVERT: B 186 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8298 (t80) REVERT: B 295 MET cc_start: 0.9082 (tpp) cc_final: 0.8764 (tpp) REVERT: B 309 ASN cc_start: 0.9160 (t0) cc_final: 0.8745 (p0) REVERT: B 311 GLU cc_start: 0.8743 (tt0) cc_final: 0.8116 (tt0) REVERT: B 436 MET cc_start: 0.9440 (mmm) cc_final: 0.9043 (mmm) REVERT: B 496 MET cc_start: 0.9380 (mmt) cc_final: 0.9041 (mmm) REVERT: B 505 MET cc_start: 0.9052 (mtt) cc_final: 0.8622 (mmm) REVERT: B 633 ASP cc_start: 0.9020 (m-30) cc_final: 0.8738 (m-30) REVERT: B 649 MET cc_start: 0.9318 (tmm) cc_final: 0.9051 (ppp) REVERT: B 670 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 696 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.7513 (t0) REVERT: B 701 GLU cc_start: 0.9283 (tt0) cc_final: 0.8788 (pt0) REVERT: B 710 VAL cc_start: 0.9528 (OUTLIER) cc_final: 0.9250 (p) REVERT: B 859 MET cc_start: 0.9441 (mmp) cc_final: 0.8952 (mmm) REVERT: B 900 GLU cc_start: 0.8913 (tp30) cc_final: 0.8440 (tm-30) REVERT: C 87 MET cc_start: 0.8041 (tmm) cc_final: 0.7670 (tmm) REVERT: C 186 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8298 (t80) REVERT: C 295 MET cc_start: 0.9085 (tpp) cc_final: 0.8766 (tpp) REVERT: C 309 ASN cc_start: 0.9160 (t0) cc_final: 0.8746 (p0) REVERT: C 311 GLU cc_start: 0.8743 (tt0) cc_final: 0.8116 (tt0) REVERT: C 436 MET cc_start: 0.9441 (mmm) cc_final: 0.9044 (mmm) REVERT: C 496 MET cc_start: 0.9380 (mmt) cc_final: 0.9040 (mmm) REVERT: C 505 MET cc_start: 0.9054 (mtt) cc_final: 0.8623 (mmm) REVERT: C 633 ASP cc_start: 0.9021 (m-30) cc_final: 0.8740 (m-30) REVERT: C 649 MET cc_start: 0.9321 (tmm) cc_final: 0.9053 (ppp) REVERT: C 670 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8677 (p) REVERT: C 696 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7513 (t0) REVERT: C 701 GLU cc_start: 0.9282 (tt0) cc_final: 0.8786 (pt0) REVERT: C 710 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9251 (p) REVERT: C 859 MET cc_start: 0.9440 (mmp) cc_final: 0.8951 (mmm) REVERT: C 900 GLU cc_start: 0.8911 (tp30) cc_final: 0.8435 (tm-30) REVERT: D 87 MET cc_start: 0.8041 (tmm) cc_final: 0.7668 (tmm) REVERT: D 186 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8297 (t80) REVERT: D 295 MET cc_start: 0.9083 (tpp) cc_final: 0.8764 (tpp) REVERT: D 309 ASN cc_start: 0.9160 (t0) cc_final: 0.8744 (p0) REVERT: D 311 GLU cc_start: 0.8740 (tt0) cc_final: 0.8113 (tt0) REVERT: D 436 MET cc_start: 0.9440 (mmm) cc_final: 0.9045 (mmm) REVERT: D 496 MET cc_start: 0.9380 (mmt) cc_final: 0.9040 (mmm) REVERT: D 505 MET cc_start: 0.9054 (mtt) cc_final: 0.8623 (mmm) REVERT: D 633 ASP cc_start: 0.9021 (m-30) cc_final: 0.8738 (m-30) REVERT: D 649 MET cc_start: 0.9313 (tmm) cc_final: 0.9048 (ppp) REVERT: D 670 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 696 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.7513 (t0) REVERT: D 701 GLU cc_start: 0.9283 (tt0) cc_final: 0.8786 (pt0) REVERT: D 710 VAL cc_start: 0.9526 (OUTLIER) cc_final: 0.9249 (p) REVERT: D 859 MET cc_start: 0.9440 (mmp) cc_final: 0.8954 (mmm) REVERT: D 900 GLU cc_start: 0.8909 (tp30) cc_final: 0.8434 (tm-30) outliers start: 67 outliers final: 36 residues processed: 336 average time/residue: 0.2709 time to fit residues: 150.8304 Evaluate side-chains 324 residues out of total 2356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 272 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 521 TYR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 264 HIS Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 264 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 521 TYR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 264 HIS Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 521 TYR Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 696 ASN Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 196 optimal weight: 0.0980 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 721 ASN B 249 HIS B 721 ASN C 249 HIS C 721 ASN D 249 HIS D 721 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068808 restraints weight = 69905.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.070995 restraints weight = 37373.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072431 restraints weight = 24673.521| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21848 Z= 0.181 Angle : 0.653 11.264 29520 Z= 0.311 Chirality : 0.040 0.333 3300 Planarity : 0.004 0.042 3712 Dihedral : 4.093 21.782 2884 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.76 % Allowed : 27.32 % Favored : 69.92 % 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: 1.61 (0.17), residues: 2644 helix: 2.21 (0.12), residues: 2012 sheet: None (None), residues: 0 loop : -2.97 (0.20), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 391 HIS 0.004 0.001 HIS C 218 PHE 0.019 0.001 PHE A 607 TYR 0.009 0.001 TYR D 131 ARG 0.001 0.000 ARG C 853 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4005.36 seconds wall clock time: 74 minutes 14.12 seconds (4454.12 seconds total)