Starting phenix.real_space_refine on Thu Feb 15 16:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e6t_30996/02_2024/7e6t_30996_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e6t_30996/02_2024/7e6t_30996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e6t_30996/02_2024/7e6t_30996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e6t_30996/02_2024/7e6t_30996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e6t_30996/02_2024/7e6t_30996_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e6t_30996/02_2024/7e6t_30996_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.098 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 74 5.16 5 C 8263 2.51 5 N 2059 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 190": "OD1" <-> "OD2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 551": "NH1" <-> "NH2" Residue "B GLU 558": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 674": "OD1" <-> "OD2" Residue "B ARG 680": "NH1" <-> "NH2" Residue "B PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 752": "NH1" <-> "NH2" Residue "B ARG 795": "NH1" <-> "NH2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 752": "NH1" <-> "NH2" Residue "A PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12741 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6306 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 29, 'TRANS': 763} Chain breaks: 3 Chain: "A" Number of atoms: 6331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6331 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 29, 'TRANS': 766} Chain breaks: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {' CA': 3, 'NAG': 2, 'PO4': 1, 'TCR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {' CA': 3, 'NAG': 2, 'PO4': 1, 'TCR': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.94, per 1000 atoms: 0.54 Number of scatterers: 12741 At special positions: 0 Unit cell: (103.87, 97.24, 185.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 74 16.00 P 2 15.00 O 2337 8.00 N 2059 7.00 C 8263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 691 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 691 " distance=2.03 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 Links applied NAG-ASN " NAG A 905 " - " ASN A 488 " " NAG A 906 " - " ASN A 541 " " NAG B 905 " - " ASN B 488 " " NAG B 906 " - " ASN B 541 " Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.1 seconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 16 sheets defined 39.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 116 through 122 removed outlier: 3.956A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 190 through 203 Processing helix chain 'B' and resid 221 through 232 removed outlier: 4.504A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.926A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.637A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 416 through 436 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 611 through 631 removed outlier: 3.947A pdb=" N VAL B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 668 removed outlier: 3.630A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 removed outlier: 4.734A pdb=" N ILE B 686 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER B 687 " --> pdb=" O PHE B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 707 removed outlier: 4.430A pdb=" N LYS B 698 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 730 through 745 Processing helix chain 'B' and resid 770 through 791 Processing helix chain 'B' and resid 803 through 820 Processing helix chain 'B' and resid 822 through 826 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 833 through 852 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.515A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.375A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.775A pdb=" N ALA A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 3.721A pdb=" N GLU A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.529A pdb=" N LYS A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 335' Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 628 through 631 No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 652 through 667 removed outlier: 3.550A pdb=" N PHE A 656 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 664 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 706 removed outlier: 3.945A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 745 removed outlier: 3.965A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 795 removed outlier: 3.686A pdb=" N LYS A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 820 removed outlier: 3.659A pdb=" N ILE A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 854 through 858 removed outlier: 4.003A pdb=" N TYR A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.639A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= C, first strand: chain 'B' and resid 211 through 214 Processing sheet with id= D, first strand: chain 'B' and resid 266 through 268 removed outlier: 6.658A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.902A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= G, first strand: chain 'B' and resid 550 through 553 Processing sheet with id= H, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= I, first strand: chain 'B' and resid 749 through 751 Processing sheet with id= J, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.074A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 211 through 214 Processing sheet with id= L, first strand: chain 'A' and resid 266 through 268 removed outlier: 6.327A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.655A pdb=" N TYR A 489 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 509 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= O, first strand: chain 'A' and resid 550 through 553 Processing sheet with id= P, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.549A pdb=" N GLU A 604 " --> pdb=" O ILE A 761 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4008 1.34 - 1.46: 3303 1.46 - 1.58: 5657 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 13056 Sorted by residual: bond pdb=" CD1 TCR A 907 " pdb=" C9 TCR A 907 " ideal model delta sigma weight residual 1.489 1.570 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CD1 TCR B 907 " pdb=" C9 TCR B 907 " ideal model delta sigma weight residual 1.489 1.570 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O3 PO4 B 901 " pdb=" P PO4 B 901 " ideal model delta sigma weight residual 1.569 1.495 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O3 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 13051 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.41: 203 105.41 - 112.55: 6569 112.55 - 119.69: 4197 119.69 - 126.84: 6568 126.84 - 133.98: 180 Bond angle restraints: 17717 Sorted by residual: angle pdb=" N TCR B 907 " pdb=" C9 TCR B 907 " pdb=" CD1 TCR B 907 " ideal model delta sigma weight residual 107.47 120.08 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" N TCR A 907 " pdb=" C9 TCR A 907 " pdb=" CD1 TCR A 907 " ideal model delta sigma weight residual 107.47 120.07 -12.60 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C GLN A 754 " pdb=" N GLU A 755 " pdb=" CA GLU A 755 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.97e+00 angle pdb=" CA SER B 402 " pdb=" C SER B 402 " pdb=" O SER B 402 " ideal model delta sigma weight residual 120.55 117.36 3.19 1.06e+00 8.90e-01 9.06e+00 angle pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" O SER A 403 " ideal model delta sigma weight residual 120.90 117.83 3.07 1.03e+00 9.43e-01 8.86e+00 ... (remaining 17712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 7117 21.24 - 42.49: 520 42.49 - 63.73: 55 63.73 - 84.98: 16 84.98 - 106.22: 14 Dihedral angle restraints: 7722 sinusoidal: 3090 harmonic: 4632 Sorted by residual: dihedral pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual -86.00 -143.53 57.53 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -129.81 43.81 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS B 661 " pdb=" SG CYS B 661 " pdb=" SG CYS B 691 " pdb=" CB CYS B 691 " ideal model delta sinusoidal sigma weight residual -86.00 -52.46 -33.54 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 7719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1632 0.051 - 0.103: 292 0.103 - 0.154: 58 0.154 - 0.205: 1 0.205 - 0.257: 1 Chirality restraints: 1984 Sorted by residual: chirality pdb=" CA ILE B 401 " pdb=" N ILE B 401 " pdb=" C ILE B 401 " pdb=" CB ILE B 401 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE A 401 " pdb=" CA ILE A 401 " pdb=" CG1 ILE A 401 " pdb=" CG2 ILE A 401 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA GLU A 755 " pdb=" N GLU A 755 " pdb=" C GLU A 755 " pdb=" CB GLU A 755 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1981 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 610 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 611 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 610 " -0.027 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 611 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.017 2.00e-02 2.50e+03 1.15e-02 2.66e+00 pdb=" CG TYR A 421 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.002 2.00e-02 2.50e+03 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 31 2.46 - 3.07: 8306 3.07 - 3.68: 18331 3.68 - 4.29: 25879 4.29 - 4.90: 43717 Nonbonded interactions: 96264 Sorted by model distance: nonbonded pdb=" OH TYR A 489 " pdb="CA CA A 902 " model vdw 1.853 2.510 nonbonded pdb=" OE1 GLU A 80 " pdb=" OH TYR A 425 " model vdw 2.191 2.440 nonbonded pdb=" O4 NAG A 905 " pdb=" O7 NAG A 905 " model vdw 2.223 2.440 nonbonded pdb=" O LEU A 87 " pdb=" NE2 GLN A 432 " model vdw 2.248 2.520 nonbonded pdb=" OG SER B 693 " pdb=" OE1 GLN B 735 " model vdw 2.266 2.440 ... (remaining 96259 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' and (resid 22 through 124 or resid 128 through 861 or resid 901 throu \ gh 907)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.460 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 35.500 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 0.081 13056 Z= 0.191 Angle : 0.545 12.610 17717 Z= 0.284 Chirality : 0.041 0.257 1984 Planarity : 0.003 0.050 2240 Dihedral : 14.783 106.222 4691 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.36 % Allowed : 0.22 % Favored : 99.42 % 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: 0.77 (0.21), residues: 1575 helix: 2.01 (0.21), residues: 592 sheet: 0.04 (0.39), residues: 193 loop : -0.52 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 818 HIS 0.003 0.000 HIS A 463 PHE 0.018 0.001 PHE A 815 TYR 0.028 0.001 TYR A 421 ARG 0.002 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 1.312 Fit side-chains REVERT: B 297 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7328 (tp30) REVERT: B 572 GLU cc_start: 0.6812 (pm20) cc_final: 0.6141 (pm20) REVERT: A 446 ASN cc_start: 0.7660 (t0) cc_final: 0.7404 (t0) REVERT: A 811 MET cc_start: 0.6845 (ppp) cc_final: 0.6626 (ppp) outliers start: 5 outliers final: 2 residues processed: 104 average time/residue: 1.1082 time to fit residues: 127.9822 Evaluate side-chains 68 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 409 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 143 optimal weight: 9.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13056 Z= 0.313 Angle : 0.593 7.851 17717 Z= 0.308 Chirality : 0.044 0.161 1984 Planarity : 0.004 0.051 2240 Dihedral : 5.824 59.125 1789 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.08 % Allowed : 7.30 % Favored : 91.61 % 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: 0.14 (0.20), residues: 1575 helix: 1.40 (0.21), residues: 606 sheet: -0.34 (0.37), residues: 196 loop : -0.83 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 206 HIS 0.005 0.001 HIS A 463 PHE 0.017 0.002 PHE B 42 TYR 0.018 0.002 TYR B 435 ARG 0.005 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.330 Fit side-chains REVERT: B 90 ASN cc_start: 0.6685 (m-40) cc_final: 0.6327 (t0) REVERT: B 572 GLU cc_start: 0.7344 (pm20) cc_final: 0.6479 (pm20) REVERT: A 340 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7093 (ttm170) REVERT: A 402 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8804 (m) REVERT: A 446 ASN cc_start: 0.7575 (t0) cc_final: 0.7304 (t0) REVERT: A 811 MET cc_start: 0.6836 (ppp) cc_final: 0.6341 (ppp) outliers start: 15 outliers final: 5 residues processed: 81 average time/residue: 0.9926 time to fit residues: 90.7075 Evaluate side-chains 62 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 580 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 39 optimal weight: 0.0570 chunk 143 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13056 Z= 0.227 Angle : 0.510 6.548 17717 Z= 0.265 Chirality : 0.042 0.186 1984 Planarity : 0.004 0.051 2240 Dihedral : 4.591 54.607 1788 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.37 % Allowed : 9.26 % Favored : 89.37 % 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: -0.06 (0.20), residues: 1575 helix: 1.29 (0.21), residues: 603 sheet: -0.56 (0.37), residues: 202 loop : -0.96 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 293 HIS 0.008 0.001 HIS B 359 PHE 0.013 0.001 PHE A 347 TYR 0.017 0.001 TYR A 421 ARG 0.003 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 1.485 Fit side-chains REVERT: B 59 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: B 90 ASN cc_start: 0.6749 (m-40) cc_final: 0.6344 (t0) REVERT: B 572 GLU cc_start: 0.7477 (pm20) cc_final: 0.6526 (pm20) REVERT: A 340 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7183 (ttm170) REVERT: A 402 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8813 (m) REVERT: A 446 ASN cc_start: 0.7468 (t0) cc_final: 0.7114 (t0) REVERT: A 576 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: A 811 MET cc_start: 0.7273 (ppp) cc_final: 0.6928 (ppp) outliers start: 19 outliers final: 6 residues processed: 74 average time/residue: 1.0935 time to fit residues: 90.9653 Evaluate side-chains 65 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 576 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 136 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 207 ASN A 359 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13056 Z= 0.364 Angle : 0.563 6.405 17717 Z= 0.298 Chirality : 0.044 0.176 1984 Planarity : 0.004 0.053 2240 Dihedral : 4.747 51.874 1788 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.52 % Allowed : 10.05 % Favored : 88.43 % 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: -0.41 (0.20), residues: 1575 helix: 1.00 (0.21), residues: 600 sheet: -0.76 (0.37), residues: 198 loop : -1.15 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 293 HIS 0.006 0.001 HIS B 359 PHE 0.017 0.001 PHE A 347 TYR 0.018 0.002 TYR A 421 ARG 0.005 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 59 time to evaluate : 1.370 Fit side-chains REVERT: B 90 ASN cc_start: 0.7025 (m-40) cc_final: 0.6519 (t0) REVERT: B 516 LYS cc_start: 0.7890 (mttp) cc_final: 0.7477 (mtpp) REVERT: B 572 GLU cc_start: 0.7839 (pm20) cc_final: 0.7262 (pm20) REVERT: A 340 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7224 (ttm170) REVERT: A 402 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8793 (m) REVERT: A 446 ASN cc_start: 0.7471 (t0) cc_final: 0.7074 (t0) REVERT: A 576 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: A 811 MET cc_start: 0.7194 (ppp) cc_final: 0.6864 (ppp) outliers start: 21 outliers final: 8 residues processed: 73 average time/residue: 1.1755 time to fit residues: 95.4469 Evaluate side-chains 68 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13056 Z= 0.214 Angle : 0.495 6.488 17717 Z= 0.259 Chirality : 0.041 0.159 1984 Planarity : 0.004 0.053 2240 Dihedral : 4.528 51.129 1788 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 10.34 % Favored : 87.78 % 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: -0.37 (0.20), residues: 1575 helix: 1.06 (0.21), residues: 602 sheet: -0.79 (0.38), residues: 198 loop : -1.14 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 208 HIS 0.006 0.001 HIS B 359 PHE 0.011 0.001 PHE A 347 TYR 0.016 0.001 TYR A 421 ARG 0.007 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 1.264 Fit side-chains REVERT: B 90 ASN cc_start: 0.6980 (m-40) cc_final: 0.6470 (t0) REVERT: B 516 LYS cc_start: 0.7884 (mttp) cc_final: 0.7476 (mtpp) REVERT: B 572 GLU cc_start: 0.7727 (pm20) cc_final: 0.7267 (pm20) REVERT: B 589 PHE cc_start: 0.6657 (m-80) cc_final: 0.6000 (m-80) REVERT: A 340 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7223 (ttm170) REVERT: A 446 ASN cc_start: 0.7461 (t0) cc_final: 0.7027 (t0) REVERT: A 734 MET cc_start: 0.8470 (ppp) cc_final: 0.6913 (tmm) REVERT: A 811 MET cc_start: 0.7160 (ppp) cc_final: 0.6841 (ppp) outliers start: 26 outliers final: 10 residues processed: 81 average time/residue: 1.0017 time to fit residues: 91.3108 Evaluate side-chains 68 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 126 optimal weight: 0.0670 chunk 70 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13056 Z= 0.154 Angle : 0.474 8.093 17717 Z= 0.244 Chirality : 0.040 0.159 1984 Planarity : 0.003 0.051 2240 Dihedral : 4.351 54.349 1788 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.74 % Allowed : 11.57 % Favored : 86.70 % 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: -0.23 (0.21), residues: 1575 helix: 1.18 (0.21), residues: 602 sheet: -0.80 (0.38), residues: 200 loop : -1.04 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 208 HIS 0.007 0.001 HIS B 359 PHE 0.009 0.001 PHE A 469 TYR 0.014 0.001 TYR B 435 ARG 0.009 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 1.445 Fit side-chains REVERT: B 90 ASN cc_start: 0.6842 (m-40) cc_final: 0.6379 (t0) REVERT: B 217 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8246 (t0) REVERT: B 516 LYS cc_start: 0.7799 (mttp) cc_final: 0.7373 (mtpp) REVERT: B 572 GLU cc_start: 0.7731 (pm20) cc_final: 0.7239 (pm20) REVERT: B 761 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6699 (tp) REVERT: A 340 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7218 (ttm170) REVERT: A 446 ASN cc_start: 0.7437 (t0) cc_final: 0.7006 (t0) REVERT: A 734 MET cc_start: 0.8457 (ppp) cc_final: 0.6943 (tmm) REVERT: A 811 MET cc_start: 0.7174 (ppp) cc_final: 0.6790 (ppp) outliers start: 24 outliers final: 11 residues processed: 75 average time/residue: 1.1889 time to fit residues: 99.4413 Evaluate side-chains 72 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 811 MET Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13056 Z= 0.250 Angle : 0.516 8.129 17717 Z= 0.267 Chirality : 0.042 0.170 1984 Planarity : 0.004 0.052 2240 Dihedral : 4.468 54.131 1786 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.59 % Allowed : 12.29 % Favored : 86.12 % 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: -0.35 (0.20), residues: 1575 helix: 1.08 (0.21), residues: 602 sheet: -0.83 (0.38), residues: 198 loop : -1.13 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.005 0.001 HIS B 359 PHE 0.013 0.001 PHE B 469 TYR 0.016 0.001 TYR A 421 ARG 0.007 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 1.278 Fit side-chains REVERT: B 90 ASN cc_start: 0.6990 (m-40) cc_final: 0.6476 (t0) REVERT: B 217 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8263 (t0) REVERT: B 516 LYS cc_start: 0.7932 (mttp) cc_final: 0.7467 (mtpp) REVERT: B 572 GLU cc_start: 0.7800 (pm20) cc_final: 0.7247 (pm20) REVERT: B 589 PHE cc_start: 0.6694 (m-80) cc_final: 0.6171 (m-80) REVERT: B 761 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6636 (tp) REVERT: A 340 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7230 (ttm170) REVERT: A 446 ASN cc_start: 0.7398 (t0) cc_final: 0.6945 (t0) REVERT: A 811 MET cc_start: 0.7137 (ppp) cc_final: 0.6760 (ppp) outliers start: 22 outliers final: 15 residues processed: 74 average time/residue: 1.0742 time to fit residues: 89.3511 Evaluate side-chains 75 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13056 Z= 0.253 Angle : 0.515 6.941 17717 Z= 0.268 Chirality : 0.042 0.157 1984 Planarity : 0.004 0.052 2240 Dihedral : 4.522 52.756 1786 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.81 % Allowed : 12.51 % Favored : 85.68 % 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: -0.42 (0.20), residues: 1575 helix: 1.04 (0.21), residues: 600 sheet: -0.90 (0.37), residues: 198 loop : -1.16 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.006 0.001 HIS B 359 PHE 0.013 0.001 PHE A 347 TYR 0.017 0.001 TYR A 421 ARG 0.007 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 1.366 Fit side-chains REVERT: B 90 ASN cc_start: 0.6999 (m-40) cc_final: 0.6473 (t0) REVERT: B 217 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8270 (t0) REVERT: B 516 LYS cc_start: 0.7950 (mttp) cc_final: 0.7488 (mtpp) REVERT: B 572 GLU cc_start: 0.7801 (pm20) cc_final: 0.7103 (pm20) REVERT: B 761 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6573 (tp) REVERT: A 340 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7215 (ttm170) REVERT: A 446 ASN cc_start: 0.7370 (t0) cc_final: 0.6899 (t0) REVERT: A 734 MET cc_start: 0.8452 (ppp) cc_final: 0.7036 (tmm) REVERT: A 811 MET cc_start: 0.7140 (ppp) cc_final: 0.6830 (ppp) outliers start: 25 outliers final: 14 residues processed: 75 average time/residue: 1.0760 time to fit residues: 90.5770 Evaluate side-chains 71 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 85 optimal weight: 0.0370 chunk 61 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 150 optimal weight: 9.9990 overall best weight: 1.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS A 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13056 Z= 0.355 Angle : 0.562 6.849 17717 Z= 0.295 Chirality : 0.044 0.185 1984 Planarity : 0.004 0.054 2240 Dihedral : 4.766 49.988 1786 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.59 % Allowed : 13.30 % Favored : 85.10 % 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: -0.63 (0.20), residues: 1575 helix: 0.87 (0.21), residues: 599 sheet: -1.05 (0.37), residues: 198 loop : -1.27 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 293 HIS 0.007 0.001 HIS B 359 PHE 0.016 0.001 PHE A 347 TYR 0.018 0.002 TYR A 421 ARG 0.006 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 1.529 Fit side-chains REVERT: B 90 ASN cc_start: 0.7008 (m-40) cc_final: 0.6561 (t0) REVERT: B 217 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8281 (t0) REVERT: B 516 LYS cc_start: 0.8018 (mttp) cc_final: 0.7534 (mtpp) REVERT: B 572 GLU cc_start: 0.7815 (pm20) cc_final: 0.7081 (pm20) REVERT: B 761 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6454 (tp) REVERT: B 771 MET cc_start: 0.5093 (mpt) cc_final: 0.4723 (mpp) REVERT: A 340 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7228 (ttm170) REVERT: A 446 ASN cc_start: 0.7311 (t0) cc_final: 0.6833 (t0) REVERT: A 734 MET cc_start: 0.8501 (ppp) cc_final: 0.7044 (tmm) outliers start: 22 outliers final: 12 residues processed: 71 average time/residue: 1.1028 time to fit residues: 88.0855 Evaluate side-chains 71 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 144 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13056 Z= 0.152 Angle : 0.484 6.878 17717 Z= 0.250 Chirality : 0.041 0.141 1984 Planarity : 0.003 0.054 2240 Dihedral : 4.423 51.398 1786 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.45 % Allowed : 13.52 % Favored : 85.03 % 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: -0.39 (0.21), residues: 1575 helix: 1.09 (0.21), residues: 600 sheet: -1.01 (0.38), residues: 200 loop : -1.13 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 208 HIS 0.007 0.001 HIS B 359 PHE 0.011 0.001 PHE B 589 TYR 0.013 0.001 TYR A 421 ARG 0.006 0.000 ARG A 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 1.351 Fit side-chains REVERT: B 217 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8270 (t0) REVERT: B 516 LYS cc_start: 0.7959 (mttp) cc_final: 0.7461 (mtpp) REVERT: B 572 GLU cc_start: 0.7814 (pm20) cc_final: 0.7126 (pm20) REVERT: B 761 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6464 (tp) REVERT: A 340 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7228 (ttm170) REVERT: A 446 ASN cc_start: 0.7371 (t0) cc_final: 0.6941 (t0) REVERT: A 734 MET cc_start: 0.8442 (ppp) cc_final: 0.6963 (tmm) outliers start: 20 outliers final: 12 residues processed: 69 average time/residue: 1.1007 time to fit residues: 85.6941 Evaluate side-chains 68 residues out of total 1383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 679 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS A 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.187624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100763 restraints weight = 15724.207| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.46 r_work: 0.3105 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13056 Z= 0.205 Angle : 0.501 8.144 17717 Z= 0.259 Chirality : 0.041 0.148 1984 Planarity : 0.004 0.053 2240 Dihedral : 4.437 52.944 1786 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.45 % Allowed : 13.67 % Favored : 84.89 % 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: -0.38 (0.21), residues: 1575 helix: 1.09 (0.21), residues: 600 sheet: -0.93 (0.38), residues: 198 loop : -1.14 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.009 0.001 HIS B 359 PHE 0.012 0.001 PHE A 469 TYR 0.016 0.001 TYR A 421 ARG 0.006 0.000 ARG A 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.71 seconds wall clock time: 59 minutes 58.27 seconds (3598.27 seconds total)