Starting phenix.real_space_refine on Sun Mar 24 01:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqm_10555/03_2024/6tqm_10555_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqm_10555/03_2024/6tqm_10555.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/6tqm_10555/03_2024/6tqm_10555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqm_10555/03_2024/6tqm_10555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqm_10555/03_2024/6tqm_10555_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqm_10555/03_2024/6tqm_10555_trim_updated.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= -0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 4 5.49 5 S 92 5.16 5 C 12586 2.51 5 N 3374 2.21 5 O 3754 1.98 5 H 19804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "F GLU 560": "OE1" <-> "OE2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F GLU 568": "OE1" <-> "OE2" Residue "F PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 613": "OD1" <-> "OD2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F GLU 669": "OE1" <-> "OE2" Residue "F TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 692": "OE1" <-> "OE2" Residue "F PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 780": "OD1" <-> "OD2" Residue "F ASP 789": "OD1" <-> "OD2" Residue "F ASP 824": "OD1" <-> "OD2" Residue "F TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 472": "OD1" <-> "OD2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ASP 538": "OD1" <-> "OD2" Residue "C ASP 550": "OD1" <-> "OD2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C GLU 567": "OE1" <-> "OE2" Residue "C ASP 575": "OD1" <-> "OD2" Residue "C TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C ASP 630": "OD1" <-> "OD2" Residue "C ASP 641": "OD1" <-> "OD2" Residue "C TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 672": "OD1" <-> "OD2" Residue "C TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "C PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 767": "OD1" <-> "OD2" Residue "C GLU 796": "OE1" <-> "OE2" Residue "C GLU 803": "OE1" <-> "OE2" Residue "C ASP 835": "OD1" <-> "OD2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 550": "OD1" <-> "OD2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B GLU 567": "OE1" <-> "OE2" Residue "B PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 755": "OD1" <-> "OD2" Residue "B ASP 767": "OD1" <-> "OD2" Residue "B GLU 803": "OE1" <-> "OE2" Residue "B ASP 824": "OD1" <-> "OD2" Residue "B ASP 830": "OD1" <-> "OD2" Residue "B ASP 835": "OD1" <-> "OD2" Residue "B ASP 838": "OD1" <-> "OD2" Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 755": "OD1" <-> "OD2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ASP 824": "OD1" <-> "OD2" Residue "A ASP 830": "OD1" <-> "OD2" Residue "A ASP 835": "OD1" <-> "OD2" Residue "A ASP 838": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39616 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6500 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain: "C" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6500 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain: "B" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "A" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'TXE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'TXE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.40, per 1000 atoms: 0.44 Number of scatterers: 39616 At special positions: 0 Unit cell: (129.95, 157.07, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 92 16.00 P 4 15.00 O 3754 8.00 N 3374 7.00 C 12586 6.00 H 19804 1.00 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: 27.41 Conformation dependent library (CDL) restraints added in 4.2 seconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4808 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 9 sheets defined 26.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.19 Creating SS restraints... Processing helix chain 'F' and resid 467 through 476 removed outlier: 3.543A pdb=" N ASP F 472 " --> pdb=" O PRO F 468 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU F 473 " --> pdb=" O ILE F 469 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE F 475 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F 476 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 492 No H-bonds generated for 'chain 'F' and resid 489 through 492' Processing helix chain 'F' and resid 500 through 506 removed outlier: 4.292A pdb=" N ALA F 506 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 532 removed outlier: 3.605A pdb=" N GLY F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 557 removed outlier: 3.713A pdb=" N ALA F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA F 552 " --> pdb=" O PRO F 548 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TRP F 556 " --> pdb=" O ALA F 552 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 658 removed outlier: 4.937A pdb=" N VAL F 655 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 676 removed outlier: 3.843A pdb=" N LEU F 676 " --> pdb=" O ASP F 672 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 672 through 676' Processing helix chain 'F' and resid 678 through 681 No H-bonds generated for 'chain 'F' and resid 678 through 681' Processing helix chain 'F' and resid 693 through 695 No H-bonds generated for 'chain 'F' and resid 693 through 695' Processing helix chain 'F' and resid 699 through 704 removed outlier: 3.602A pdb=" N VAL F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 699 through 704' Processing helix chain 'F' and resid 707 through 714 removed outlier: 3.589A pdb=" N ILE F 712 " --> pdb=" O THR F 708 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 730 Processing helix chain 'F' and resid 739 through 743 Processing helix chain 'F' and resid 745 through 748 No H-bonds generated for 'chain 'F' and resid 745 through 748' Processing helix chain 'F' and resid 773 through 781 removed outlier: 3.840A pdb=" N ILE F 778 " --> pdb=" O ARG F 774 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA F 779 " --> pdb=" O TYR F 775 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS F 781 " --> pdb=" O GLU F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 791 through 809 removed outlier: 3.562A pdb=" N ILE F 795 " --> pdb=" O THR F 791 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU F 796 " --> pdb=" O ALA F 792 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 797 " --> pdb=" O ALA F 793 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP F 801 " --> pdb=" O LYS F 797 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 805 " --> pdb=" O TRP F 801 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 806 " --> pdb=" O LEU F 802 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU F 808 " --> pdb=" O THR F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 818 Processing helix chain 'F' and resid 830 through 833 No H-bonds generated for 'chain 'F' and resid 830 through 833' Processing helix chain 'F' and resid 857 through 860 No H-bonds generated for 'chain 'F' and resid 857 through 860' Processing helix chain 'C' and resid 467 through 476 removed outlier: 3.896A pdb=" N ASP C 472 " --> pdb=" O PRO C 468 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 473 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 498 through 504 removed outlier: 4.143A pdb=" N VAL C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 503 " --> pdb=" O ILE C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.962A pdb=" N SER C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 560 removed outlier: 3.654A pdb=" N ALA C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 560 " --> pdb=" O TRP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 650 through 658 removed outlier: 4.307A pdb=" N VAL C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 699 through 705 removed outlier: 3.586A pdb=" N VAL C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 713 No H-bonds generated for 'chain 'C' and resid 710 through 713' Processing helix chain 'C' and resid 722 through 729 removed outlier: 3.913A pdb=" N ALA C 726 " --> pdb=" O CYS C 722 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 728 " --> pdb=" O SER C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 781 removed outlier: 3.512A pdb=" N GLU C 777 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 778 " --> pdb=" O TYR C 775 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS C 781 " --> pdb=" O ILE C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 791 through 808 removed outlier: 3.540A pdb=" N ILE C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 801 " --> pdb=" O LYS C 797 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 804 " --> pdb=" O ALA C 800 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 808 " --> pdb=" O THR C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 838 removed outlier: 4.634A pdb=" N ASP C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 836 " --> pdb=" O LEU C 832 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 860 removed outlier: 3.661A pdb=" N LYS C 855 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 23 removed outlier: 4.020A pdb=" N ASN B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 118 through 121 No H-bonds generated for 'chain 'B' and resid 118 through 121' Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.657A pdb=" N ASP B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 199 through 202 No H-bonds generated for 'chain 'B' and resid 199 through 202' Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.631A pdb=" N HIS B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.926A pdb=" N VAL B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN B 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 4.081A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.962A pdb=" N GLU B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 3.501A pdb=" N ALA B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 363' Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.643A pdb=" N PHE B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 381 through 386' Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.780A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 501 through 504 No H-bonds generated for 'chain 'B' and resid 501 through 504' Processing helix chain 'B' and resid 524 through 534 removed outlier: 4.089A pdb=" N SER B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 552 No H-bonds generated for 'chain 'B' and resid 549 through 552' Processing helix chain 'B' and resid 651 through 658 removed outlier: 3.563A pdb=" N VAL B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 682 removed outlier: 3.586A pdb=" N ALA B 678 " --> pdb=" O GLN B 674 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 691 No H-bonds generated for 'chain 'B' and resid 688 through 691' Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.515A pdb=" N VAL B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 703' Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 722 through 729 removed outlier: 3.961A pdb=" N ALA B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N HIS B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 749 through 751 No H-bonds generated for 'chain 'B' and resid 749 through 751' Processing helix chain 'B' and resid 773 through 781 removed outlier: 3.598A pdb=" N GLU B 777 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE B 778 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS B 781 " --> pdb=" O ILE B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 804 removed outlier: 3.843A pdb=" N ILE B 795 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP B 801 " --> pdb=" O LYS B 797 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 817 No H-bonds generated for 'chain 'B' and resid 815 through 817' Processing helix chain 'B' and resid 830 through 833 No H-bonds generated for 'chain 'B' and resid 830 through 833' Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'A' and resid 6 through 23 removed outlier: 4.020A pdb=" N ASN A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 118 through 121 No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.656A pdb=" N ASP A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 199 through 202 No H-bonds generated for 'chain 'A' and resid 199 through 202' Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.631A pdb=" N HIS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.926A pdb=" N VAL A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 4.081A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.962A pdb=" N GLU A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.501A pdb=" N ALA A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 357 through 363' Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.644A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 386' Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.779A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 501 through 504 No H-bonds generated for 'chain 'A' and resid 501 through 504' Processing helix chain 'A' and resid 524 through 534 removed outlier: 4.089A pdb=" N SER A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 651 through 658 removed outlier: 3.561A pdb=" N VAL A 655 " --> pdb=" O GLY A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.586A pdb=" N ALA A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 691 No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.516A pdb=" N VAL A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 703' Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 722 through 729 removed outlier: 3.960A pdb=" N ALA A 726 " --> pdb=" O CYS A 722 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N HIS A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.597A pdb=" N GLU A 777 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 778 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 781 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.844A pdb=" N ILE A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 830 through 833 No H-bonds generated for 'chain 'A' and resid 830 through 833' Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing sheet with id= A, first strand: chain 'F' and resid 539 through 541 removed outlier: 6.911A pdb=" N LYS F 591 " --> pdb=" O ILE F 540 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'F' and resid 609 through 612 removed outlier: 3.675A pdb=" N ALA F 609 " --> pdb=" O LEU F 622 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 611 " --> pdb=" O TYR F 620 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 539 through 541 removed outlier: 6.528A pdb=" N LYS C 591 " --> pdb=" O ILE C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.637A pdb=" N LEU B 189 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 210 " --> pdb=" O ALA B 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 370 through 372 removed outlier: 3.619A pdb=" N CYS B 370 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 250 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 219 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 252 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE B 221 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL B 254 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 254 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.888A pdb=" N GLU B 511 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 539 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.638A pdb=" N LEU A 189 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 210 " --> pdb=" O ALA A 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 370 through 372 removed outlier: 3.619A pdb=" N CYS A 370 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 250 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL A 219 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 252 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 221 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 254 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 254 " --> pdb=" O TYR A 344 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.888A pdb=" N GLU A 511 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 539 " --> pdb=" O LEU A 483 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 441 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: 12.05 Time building geometry restraints manager: 28.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19778 1.03 - 1.23: 63 1.23 - 1.42: 8236 1.42 - 1.62: 11773 1.62 - 1.81: 170 Bond restraints: 40020 Sorted by residual: bond pdb=" C1' TXE A 902 " pdb=" C2' TXE A 902 " ideal model delta sigma weight residual 1.530 1.296 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1' TXE B 902 " pdb=" C2' TXE B 902 " ideal model delta sigma weight residual 1.530 1.297 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1' TXE A 902 " pdb=" O4' TXE A 902 " ideal model delta sigma weight residual 1.396 1.628 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' TXE B 902 " pdb=" O4' TXE B 902 " ideal model delta sigma weight residual 1.396 1.628 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1B TXE B 902 " pdb=" C2B TXE B 902 " ideal model delta sigma weight residual 1.534 1.311 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 40015 not shown) Histogram of bond angle deviations from ideal: 97.43 - 105.11: 416 105.11 - 112.78: 47146 112.78 - 120.45: 14226 120.45 - 128.12: 10553 128.12 - 135.79: 209 Bond angle restraints: 72550 Sorted by residual: angle pdb=" O1N TXE A 902 " pdb=" PN TXE A 902 " pdb=" O2N TXE A 902 " ideal model delta sigma weight residual 121.99 107.77 14.22 3.00e+00 1.11e-01 2.25e+01 angle pdb=" O1N TXE B 902 " pdb=" PN TXE B 902 " pdb=" O2N TXE B 902 " ideal model delta sigma weight residual 121.99 107.90 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" N1A TXE B 902 " pdb=" C6A TXE B 902 " pdb=" N6A TXE B 902 " ideal model delta sigma weight residual 119.31 106.01 13.30 3.00e+00 1.11e-01 1.96e+01 angle pdb=" N1A TXE A 902 " pdb=" C6A TXE A 902 " pdb=" N6A TXE A 902 " ideal model delta sigma weight residual 119.31 106.03 13.28 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C PRO B 138 " pdb=" N HIS B 139 " pdb=" CA HIS B 139 " ideal model delta sigma weight residual 120.97 133.35 -12.38 2.84e+00 1.24e-01 1.90e+01 ... (remaining 72545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 16731 17.39 - 34.78: 1632 34.78 - 52.18: 384 52.18 - 69.57: 146 69.57 - 86.96: 43 Dihedral angle restraints: 18936 sinusoidal: 10336 harmonic: 8600 Sorted by residual: dihedral pdb=" CA ILE B 47 " pdb=" C ILE B 47 " pdb=" N PRO B 48 " pdb=" CA PRO B 48 " ideal model delta harmonic sigma weight residual 180.00 135.72 44.28 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA ILE A 47 " pdb=" C ILE A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA PHE C 462 " pdb=" C PHE C 462 " pdb=" N ARG C 463 " pdb=" CA ARG C 463 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 18933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.808: 3132 0.808 - 1.617: 0 1.617 - 2.425: 0 2.425 - 3.234: 0 3.234 - 4.042: 2 Chirality restraints: 3134 Sorted by residual: chirality pdb=" C3N TXE B 902 " pdb=" C2N TXE B 902 " pdb=" C4N TXE B 902 " pdb=" C7N TXE B 902 " both_signs ideal model delta sigma weight residual False -2.69 1.35 -4.04 2.00e-01 2.50e+01 4.08e+02 chirality pdb=" C3N TXE A 902 " pdb=" C2N TXE A 902 " pdb=" C4N TXE A 902 " pdb=" C7N TXE A 902 " both_signs ideal model delta sigma weight residual False -2.69 1.35 -4.04 2.00e-01 2.50e+01 4.08e+02 chirality pdb=" CB THR B 324 " pdb=" CA THR B 324 " pdb=" OG1 THR B 324 " pdb=" CG2 THR B 324 " both_signs ideal model delta sigma weight residual False 2.55 2.00 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 3131 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 47 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO B 48 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 48 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 48 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 47 " -0.051 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO A 48 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 714 " -0.025 2.00e-02 2.50e+03 1.44e-02 6.22e+00 pdb=" CG PHE B 714 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 714 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 714 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 714 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 714 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 714 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 714 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 714 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 714 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 714 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 714 " -0.000 2.00e-02 2.50e+03 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2775 2.21 - 2.81: 83158 2.81 - 3.40: 87652 3.40 - 4.00: 119992 4.00 - 4.60: 187345 Nonbonded interactions: 480922 Sorted by model distance: nonbonded pdb=" OE1 GLN A 760 " pdb=" HG SER A 764 " model vdw 1.612 1.850 nonbonded pdb=" OE1 GLN B 760 " pdb=" HG SER B 764 " model vdw 1.613 1.850 nonbonded pdb=" OD1 ASP A 497 " pdb=" H ASP A 497 " model vdw 1.633 1.850 nonbonded pdb=" OD1 ASP B 497 " pdb=" H ASP B 497 " model vdw 1.634 1.850 nonbonded pdb="HH21 ARG B 46 " pdb=" OD2 ASP A 838 " model vdw 1.637 1.850 ... (remaining 480917 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' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.620 Extract box with map and model: 5.900 Check model and map are aligned: 0.570 Set scattering table: 0.310 Process input model: 111.660 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0650 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 : 0.014 0.234 20216 Z= 0.903 Angle : 0.977 14.219 27434 Z= 0.492 Chirality : 0.119 4.042 3134 Planarity : 0.006 0.076 3540 Dihedral : 16.139 86.962 7498 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 1.40 % Allowed : 3.67 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -5.95 (0.13), residues: 2570 helix: -4.75 (0.08), residues: 836 sheet: -3.31 (0.24), residues: 308 loop : -3.68 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 453 HIS 0.007 0.002 HIS B 184 PHE 0.043 0.003 PHE B 714 TYR 0.017 0.002 TYR A 77 ARG 0.008 0.001 ARG F 750 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 242 time to evaluate : 2.807 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: symmetry clash 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: symmetry clash 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: F 604 GLU cc_start: 0.5442 (pm20) cc_final: 0.4734 (mm-30) REVERT: C 826 LEU cc_start: 0.3720 (mp) cc_final: 0.3379 (tt) REVERT: B 408 LEU cc_start: 0.6358 (mp) cc_final: 0.5843 (tt) REVERT: B 530 GLU cc_start: -0.3461 (OUTLIER) cc_final: -0.4135 (mt-10) REVERT: B 574 MET cc_start: 0.1152 (ptt) cc_final: 0.0639 (ttp) REVERT: B 606 THR cc_start: 0.1050 (t) cc_final: -0.0946 (p) REVERT: B 640 MET cc_start: -0.2849 (mmt) cc_final: -0.3117 (mmt) REVERT: B 755 ASP cc_start: -0.5595 (OUTLIER) cc_final: -0.6674 (t70) REVERT: A 112 PRO cc_start: 0.3453 (Cg_endo) cc_final: 0.3252 (Cg_exo) REVERT: A 372 TYR cc_start: -0.2713 (m-80) cc_final: -0.4918 (m-80) REVERT: A 417 LEU cc_start: 0.2691 (pt) cc_final: 0.1969 (mp) outliers start: 29 outliers final: 9 residues processed: 270 average time/residue: 0.7253 time to fit residues: 301.3745 Evaluate side-chains 181 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 840 GLN C 450 ASN C 657 HIS C 674 GLN C 752 ASN C 756 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 732 GLN A 283 GLN A 618 GLN A 732 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0908 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20216 Z= 0.166 Angle : 0.577 7.951 27434 Z= 0.297 Chirality : 0.042 0.175 3134 Planarity : 0.004 0.069 3540 Dihedral : 7.944 84.889 2918 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.01 % Allowed : 8.45 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -5.17 (0.14), residues: 2570 helix: -3.96 (0.12), residues: 818 sheet: -3.03 (0.25), residues: 330 loop : -3.26 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 424 HIS 0.013 0.001 HIS F 657 PHE 0.021 0.001 PHE F 714 TYR 0.014 0.001 TYR F 620 ARG 0.003 0.000 ARG F 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 2.870 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 659 MET cc_start: -0.1152 (tmm) cc_final: -0.2388 (mmm) REVERT: C 543 LEU cc_start: 0.4921 (mt) cc_final: 0.4708 (mt) REVERT: C 573 PHE cc_start: 0.2642 (OUTLIER) cc_final: 0.1363 (m-80) REVERT: C 586 MET cc_start: -0.2316 (mtp) cc_final: -0.2523 (mtp) REVERT: B 182 MET cc_start: -0.4905 (mtp) cc_final: -0.5121 (mtt) REVERT: B 410 ASN cc_start: 0.0529 (t0) cc_final: 0.0127 (t0) REVERT: B 574 MET cc_start: 0.0311 (ptt) cc_final: -0.0126 (ttp) REVERT: B 606 THR cc_start: 0.1147 (t) cc_final: -0.0777 (p) REVERT: A 236 MET cc_start: 0.2685 (ttp) cc_final: 0.2139 (ttp) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 0.7245 time to fit residues: 217.3281 Evaluate side-chains 175 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 821 GLN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.0010 chunk 72 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 230 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN C 737 HIS ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1047 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20216 Z= 0.140 Angle : 0.514 5.265 27434 Z= 0.266 Chirality : 0.040 0.144 3134 Planarity : 0.004 0.066 3540 Dihedral : 6.745 83.023 2907 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.21 % Allowed : 9.36 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -4.47 (0.15), residues: 2570 helix: -3.28 (0.14), residues: 798 sheet: -2.69 (0.26), residues: 330 loop : -2.90 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 801 HIS 0.007 0.001 HIS F 657 PHE 0.019 0.001 PHE C 714 TYR 0.008 0.001 TYR A 559 ARG 0.007 0.000 ARG B 790 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 2.927 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 659 MET cc_start: -0.0790 (tmm) cc_final: -0.1052 (mmm) REVERT: C 543 LEU cc_start: 0.5062 (mt) cc_final: 0.4835 (mt) REVERT: C 573 PHE cc_start: 0.2748 (OUTLIER) cc_final: 0.1392 (m-80) REVERT: C 586 MET cc_start: -0.2757 (mtp) cc_final: -0.2991 (mtp) REVERT: C 826 LEU cc_start: 0.6049 (pt) cc_final: 0.4280 (tt) REVERT: B 182 MET cc_start: -0.4571 (mtp) cc_final: -0.4877 (mtt) REVERT: B 574 MET cc_start: 0.0288 (ptt) cc_final: -0.0430 (ttm) REVERT: B 606 THR cc_start: 0.1598 (t) cc_final: -0.0218 (p) REVERT: A 122 PHE cc_start: 0.3920 (t80) cc_final: 0.3214 (t80) REVERT: A 236 MET cc_start: 0.2486 (ttp) cc_final: 0.2265 (ttp) REVERT: A 555 MET cc_start: -0.4072 (OUTLIER) cc_final: -0.4384 (tmm) outliers start: 25 outliers final: 17 residues processed: 183 average time/residue: 0.6791 time to fit residues: 197.8361 Evaluate side-chains 178 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 732 GLN Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 233 optimal weight: 0.0670 chunk 247 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 221 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 450 ASN F 716 ASN C 756 ASN B 30 GLN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2197 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.158 20216 Z= 0.479 Angle : 1.038 11.833 27434 Z= 0.555 Chirality : 0.054 0.247 3134 Planarity : 0.007 0.087 3540 Dihedral : 9.657 74.984 2903 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.00 % Favored : 86.93 % Rotamer: Outliers : 2.94 % Allowed : 12.16 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.14), residues: 2570 helix: -3.46 (0.14), residues: 762 sheet: -2.85 (0.28), residues: 270 loop : -3.22 (0.14), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 801 HIS 0.029 0.003 HIS F 737 PHE 0.064 0.004 PHE C 714 TYR 0.037 0.003 TYR B 662 ARG 0.014 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 166 time to evaluate : 2.956 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: F 483 LEU cc_start: 0.2088 (OUTLIER) cc_final: 0.1634 (tt) REVERT: F 640 MET cc_start: 0.2429 (mmt) cc_final: 0.1596 (mmt) REVERT: F 741 ASN cc_start: -0.0132 (OUTLIER) cc_final: -0.1410 (p0) REVERT: C 550 ASP cc_start: 0.0612 (OUTLIER) cc_final: 0.0318 (m-30) REVERT: C 630 ASP cc_start: 0.7108 (m-30) cc_final: 0.6708 (m-30) REVERT: C 824 ASP cc_start: 0.4930 (p0) cc_final: 0.4566 (t0) REVERT: B 182 MET cc_start: -0.4509 (mtp) cc_final: -0.4898 (mtt) REVERT: B 444 VAL cc_start: -0.4835 (OUTLIER) cc_final: -0.5294 (t) REVERT: B 574 MET cc_start: 0.0682 (ptt) cc_final: 0.0433 (ptt) REVERT: A 74 GLU cc_start: -0.2367 (OUTLIER) cc_final: -0.3702 (mt-10) outliers start: 61 outliers final: 35 residues processed: 212 average time/residue: 0.6697 time to fit residues: 221.5652 Evaluate side-chains 182 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 741 ASN Chi-restraints excluded: chain F residue 837 PHE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 3 optimal weight: 0.0870 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 0.0980 chunk 171 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 716 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS B 723 HIS ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1918 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20216 Z= 0.155 Angle : 0.562 5.011 27434 Z= 0.295 Chirality : 0.042 0.144 3134 Planarity : 0.004 0.061 3540 Dihedral : 7.128 75.389 2901 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.50 % Allowed : 14.29 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -4.34 (0.14), residues: 2570 helix: -2.99 (0.15), residues: 820 sheet: -2.55 (0.29), residues: 284 loop : -2.96 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 801 HIS 0.006 0.001 HIS A 479 PHE 0.014 0.001 PHE B 462 TYR 0.018 0.001 TYR A 559 ARG 0.004 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 2.907 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 640 MET cc_start: 0.2391 (mmt) cc_final: 0.1653 (mmt) REVERT: C 543 LEU cc_start: 0.6296 (mt) cc_final: 0.5658 (mp) REVERT: B 182 MET cc_start: -0.4186 (mtp) cc_final: -0.4441 (mtt) REVERT: B 252 VAL cc_start: 0.6980 (t) cc_final: 0.6543 (p) REVERT: B 396 ILE cc_start: 0.4636 (mm) cc_final: 0.4388 (tp) REVERT: B 437 HIS cc_start: 0.0523 (OUTLIER) cc_final: -0.0235 (p90) REVERT: B 444 VAL cc_start: -0.4970 (OUTLIER) cc_final: -0.5258 (t) REVERT: A 631 MET cc_start: -0.3335 (OUTLIER) cc_final: -0.3565 (ttm) outliers start: 31 outliers final: 24 residues processed: 165 average time/residue: 0.7202 time to fit residues: 184.4028 Evaluate side-chains 168 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 760 GLN Chi-restraints excluded: chain A residue 845 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 454 HIS ** F 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN A 78 ASN ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2518 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 20216 Z= 0.415 Angle : 0.877 9.308 27434 Z= 0.474 Chirality : 0.049 0.276 3134 Planarity : 0.006 0.084 3540 Dihedral : 8.841 74.843 2901 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.44 % Favored : 85.53 % Rotamer: Outliers : 3.14 % Allowed : 14.67 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.14), residues: 2570 helix: -2.96 (0.16), residues: 800 sheet: -2.71 (0.28), residues: 276 loop : -3.23 (0.14), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 801 HIS 0.019 0.003 HIS F 737 PHE 0.039 0.003 PHE B 608 TYR 0.038 0.003 TYR C 775 ARG 0.014 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 148 time to evaluate : 2.815 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 592 MET cc_start: 0.1543 (ttt) cc_final: 0.1298 (ttt) REVERT: F 640 MET cc_start: 0.2485 (mmt) cc_final: 0.2042 (mmt) REVERT: C 543 LEU cc_start: 0.6978 (mt) cc_final: 0.6132 (mp) REVERT: B 28 GLN cc_start: 0.6633 (tp40) cc_final: 0.5675 (tm-30) REVERT: B 182 MET cc_start: -0.3566 (mtp) cc_final: -0.3772 (mtt) REVERT: B 444 VAL cc_start: -0.4273 (OUTLIER) cc_final: -0.4730 (t) REVERT: A 54 VAL cc_start: -0.1359 (OUTLIER) cc_final: -0.1794 (m) REVERT: A 444 VAL cc_start: 0.5275 (OUTLIER) cc_final: 0.5067 (m) REVERT: A 530 GLU cc_start: 0.2644 (OUTLIER) cc_final: 0.2429 (mt-10) REVERT: A 631 MET cc_start: -0.1534 (OUTLIER) cc_final: -0.2090 (ttm) outliers start: 65 outliers final: 44 residues processed: 196 average time/residue: 0.6977 time to fit residues: 212.6732 Evaluate side-chains 186 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2396 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20216 Z= 0.207 Angle : 0.622 6.275 27434 Z= 0.330 Chirality : 0.042 0.155 3134 Planarity : 0.005 0.070 3540 Dihedral : 7.847 70.575 2901 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.41 % Allowed : 15.97 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.15), residues: 2570 helix: -2.63 (0.16), residues: 820 sheet: -2.42 (0.29), residues: 274 loop : -3.03 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 801 HIS 0.007 0.001 HIS B 367 PHE 0.020 0.002 PHE A 122 TYR 0.019 0.001 TYR A 559 ARG 0.004 0.000 ARG B 772 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 2.792 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 463 ARG cc_start: -0.0448 (OUTLIER) cc_final: -0.0800 (tpp-160) REVERT: F 640 MET cc_start: 0.2066 (mmt) cc_final: 0.1791 (mmt) REVERT: F 659 MET cc_start: -0.2000 (mmm) cc_final: -0.2269 (mmm) REVERT: C 543 LEU cc_start: 0.6400 (mt) cc_final: 0.5640 (mp) REVERT: C 816 ARG cc_start: -0.3533 (ttp-170) cc_final: -0.4857 (tpt170) REVERT: B 30 GLN cc_start: 0.4131 (OUTLIER) cc_final: 0.3691 (pt0) REVERT: B 182 MET cc_start: -0.3460 (mtp) cc_final: -0.3683 (mtt) REVERT: B 444 VAL cc_start: -0.4575 (OUTLIER) cc_final: -0.4911 (t) REVERT: B 770 GLN cc_start: -0.3757 (OUTLIER) cc_final: -0.4019 (tp40) REVERT: A 631 MET cc_start: -0.2086 (OUTLIER) cc_final: -0.2570 (ttm) outliers start: 50 outliers final: 40 residues processed: 182 average time/residue: 0.7206 time to fit residues: 201.7616 Evaluate side-chains 188 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0970 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2357 moved from start: 0.8150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 20216 Z= 0.168 Angle : 0.567 7.288 27434 Z= 0.297 Chirality : 0.041 0.143 3134 Planarity : 0.004 0.064 3540 Dihedral : 7.181 69.988 2901 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.27 % Allowed : 16.26 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -3.88 (0.15), residues: 2570 helix: -2.37 (0.17), residues: 812 sheet: -2.14 (0.31), residues: 270 loop : -2.89 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 801 HIS 0.005 0.001 HIS B 367 PHE 0.019 0.001 PHE F 837 TYR 0.016 0.001 TYR A 559 ARG 0.004 0.000 ARG B 772 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 3.050 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 463 ARG cc_start: -0.0400 (OUTLIER) cc_final: -0.0698 (tpp-160) REVERT: F 640 MET cc_start: 0.2247 (mmt) cc_final: 0.1956 (mmt) REVERT: C 543 LEU cc_start: 0.6323 (mt) cc_final: 0.5539 (mp) REVERT: C 816 ARG cc_start: -0.3446 (ttp-170) cc_final: -0.4877 (tpt170) REVERT: B 182 MET cc_start: -0.3465 (mtp) cc_final: -0.3685 (mtt) REVERT: B 252 VAL cc_start: 0.6850 (t) cc_final: 0.6445 (p) REVERT: B 444 VAL cc_start: -0.4923 (OUTLIER) cc_final: -0.5234 (t) REVERT: B 463 ARG cc_start: 0.0532 (OUTLIER) cc_final: -0.0610 (tpt90) REVERT: B 770 GLN cc_start: -0.3677 (OUTLIER) cc_final: -0.3894 (tp40) REVERT: A 631 MET cc_start: -0.1809 (OUTLIER) cc_final: -0.2443 (ttm) outliers start: 47 outliers final: 35 residues processed: 180 average time/residue: 0.7387 time to fit residues: 204.7289 Evaluate side-chains 183 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 838 ASP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2402 moved from start: 0.8598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20216 Z= 0.178 Angle : 0.563 6.405 27434 Z= 0.295 Chirality : 0.041 0.146 3134 Planarity : 0.004 0.063 3540 Dihedral : 6.750 69.486 2901 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.08 % Allowed : 16.46 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -3.63 (0.16), residues: 2570 helix: -2.17 (0.18), residues: 832 sheet: -2.09 (0.31), residues: 278 loop : -2.70 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 801 HIS 0.004 0.001 HIS A 561 PHE 0.017 0.001 PHE F 837 TYR 0.016 0.001 TYR A 559 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 3.278 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: F 463 ARG cc_start: -0.0481 (OUTLIER) cc_final: -0.0810 (tpp-160) REVERT: F 640 MET cc_start: 0.2621 (mmt) cc_final: 0.2127 (mmt) REVERT: F 741 ASN cc_start: -0.0088 (OUTLIER) cc_final: -0.1844 (p0) REVERT: C 543 LEU cc_start: 0.6175 (mt) cc_final: 0.5401 (mp) REVERT: B 252 VAL cc_start: 0.6158 (t) cc_final: 0.5741 (p) REVERT: B 408 LEU cc_start: 0.6560 (mp) cc_final: 0.5563 (tt) REVERT: B 463 ARG cc_start: 0.0389 (OUTLIER) cc_final: -0.0868 (tpt90) REVERT: B 770 GLN cc_start: -0.3527 (OUTLIER) cc_final: -0.3902 (tp40) REVERT: A 59 MET cc_start: 0.4275 (ppp) cc_final: 0.3969 (ppp) outliers start: 43 outliers final: 36 residues processed: 177 average time/residue: 0.7230 time to fit residues: 197.9304 Evaluate side-chains 181 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 741 ASN Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 838 ASP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 184 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 0.0270 chunk 161 optimal weight: 8.9990 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2553 moved from start: 0.9242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20216 Z= 0.218 Angle : 0.618 10.136 27434 Z= 0.323 Chirality : 0.042 0.168 3134 Planarity : 0.004 0.068 3540 Dihedral : 7.190 68.716 2901 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 2.17 % Allowed : 16.75 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.04 % 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: -3.56 (0.16), residues: 2570 helix: -2.03 (0.18), residues: 789 sheet: -1.96 (0.33), residues: 235 loop : -2.73 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 801 HIS 0.010 0.001 HIS B 367 PHE 0.020 0.002 PHE B 566 TYR 0.024 0.001 TYR B 23 ARG 0.017 0.001 ARG B 816 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 2.751 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: F 586 MET cc_start: 0.2416 (mmm) cc_final: 0.2094 (mmm) REVERT: F 640 MET cc_start: 0.2636 (mmt) cc_final: 0.2155 (mmt) REVERT: C 543 LEU cc_start: 0.6417 (mt) cc_final: 0.5920 (mp) REVERT: B 252 VAL cc_start: 0.6247 (t) cc_final: 0.5811 (p) REVERT: B 365 ILE cc_start: 0.1905 (mm) cc_final: 0.1593 (mp) REVERT: B 408 LEU cc_start: 0.6528 (mp) cc_final: 0.5648 (tt) REVERT: B 568 GLU cc_start: 0.5191 (tt0) cc_final: 0.3960 (mt-10) REVERT: B 659 MET cc_start: 0.6138 (ppp) cc_final: 0.5806 (ppp) REVERT: B 770 GLN cc_start: -0.2354 (OUTLIER) cc_final: -0.2771 (tp40) REVERT: A 59 MET cc_start: 0.4153 (ppp) cc_final: 0.3891 (ppp) outliers start: 45 outliers final: 40 residues processed: 177 average time/residue: 0.7058 time to fit residues: 192.7585 Evaluate side-chains 181 residues out of total 2072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 838 ASP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 37 optimal weight: 8.9990 chunk 178 optimal weight: 0.0870 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5270 r_free = 0.5270 target = 0.258601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5220 r_free = 0.5220 target = 0.249364 restraints weight = 287743.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5254 r_free = 0.5254 target = 0.251913 restraints weight = 151735.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.253357 restraints weight = 86652.405| |-----------------------------------------------------------------------------| r_work (final): 0.5157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2433 moved from start: 0.9412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20216 Z= 0.176 Angle : 0.569 7.563 27434 Z= 0.296 Chirality : 0.041 0.145 3134 Planarity : 0.004 0.066 3540 Dihedral : 6.821 64.837 2901 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 1.93 % Allowed : 16.99 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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: -3.43 (0.16), residues: 2570 helix: -1.93 (0.18), residues: 803 sheet: -1.87 (0.33), residues: 248 loop : -2.64 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 801 HIS 0.005 0.001 HIS A 561 PHE 0.021 0.001 PHE C 462 TYR 0.018 0.001 TYR B 23 ARG 0.004 0.000 ARG B 772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6563.27 seconds wall clock time: 118 minutes 2.48 seconds (7082.48 seconds total)