Starting phenix.real_space_refine on Mon Aug 5 10:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k98_36980/08_2024/8k98_36980.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k98_36980/08_2024/8k98_36980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k98_36980/08_2024/8k98_36980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k98_36980/08_2024/8k98_36980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k98_36980/08_2024/8k98_36980.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k98_36980/08_2024/8k98_36980.cif" } resolution = 2.9 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= 0.001 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 8678 2.51 5 N 2147 2.21 5 O 2538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 822": "OE1" <-> "OE2" Residue "C PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "B GLU 880": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13415 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 4 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5812 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 687} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 890 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 5838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5838 Classifications: {'peptide': 698} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 688} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 7.77, per 1000 atoms: 0.58 Number of scatterers: 13415 At special positions: 0 Unit cell: (104.55, 121.55, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2538 8.00 N 2147 7.00 C 8678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.4 seconds 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 4 sheets defined 63.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 307 through 317 removed outlier: 4.253A pdb=" N TYR C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.520A pdb=" N ALA C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 322 " --> pdb=" O LEU C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 322' Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 356 through 366 removed outlier: 4.286A pdb=" N PHE C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 361 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.950A pdb=" N LYS C 372 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 373 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.672A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 447 through 465 removed outlier: 3.553A pdb=" N SER C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 495 removed outlier: 3.736A pdb=" N TYR C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 508 through 520 removed outlier: 3.549A pdb=" N LEU C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 540 through 546 removed outlier: 4.307A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 572 Processing helix chain 'C' and resid 579 through 598 Processing helix chain 'C' and resid 605 through 628 removed outlier: 3.996A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 639 Processing helix chain 'C' and resid 648 through 659 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 672 through 676 Processing helix chain 'C' and resid 680 through 700 Processing helix chain 'C' and resid 705 through 723 removed outlier: 4.718A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 743 removed outlier: 3.532A pdb=" N TYR C 743 " --> pdb=" O ALA C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 761 removed outlier: 3.559A pdb=" N LEU C 761 " --> pdb=" O TRP C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.751A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.015A pdb=" N ILE C 823 " --> pdb=" O ARG C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 841 removed outlier: 3.623A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 removed outlier: 3.838A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 880 through 903 removed outlier: 3.836A pdb=" N LEU C 884 " --> pdb=" O GLU C 880 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 893 " --> pdb=" O LEU C 889 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL C 898 " --> pdb=" O VAL C 894 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU C 901 " --> pdb=" O ILE C 897 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS C 902 " --> pdb=" O VAL C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 927 through 933 removed outlier: 4.485A pdb=" N PHE C 933 " --> pdb=" O MET C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 944 removed outlier: 4.053A pdb=" N PHE C 943 " --> pdb=" O GLN C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 962 removed outlier: 4.624A pdb=" N LYS C 960 " --> pdb=" O PRO C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 975 through 990 removed outlier: 4.231A pdb=" N HIS C 979 " --> pdb=" O HIS C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1002 removed outlier: 3.689A pdb=" N LEU C 997 " --> pdb=" O ASP C 993 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C1000 " --> pdb=" O TYR C 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.308A pdb=" N TYR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 312 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.944A pdb=" N LEU B 322 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 356 through 366 removed outlier: 4.227A pdb=" N PHE B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.951A pdb=" N LYS B 372 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 373 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.671A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 466 removed outlier: 3.545A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 494 removed outlier: 3.539A pdb=" N GLY B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'B' and resid 508 through 520 removed outlier: 3.555A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.300A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 572 Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 605 through 629 removed outlier: 3.990A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 639 Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.072A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.637A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.523A pdb=" N TYR B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 761 removed outlier: 3.564A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 803 through 812 removed outlier: 3.704A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 825 removed outlier: 3.981A pdb=" N ILE B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 841 removed outlier: 3.624A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 857 removed outlier: 3.814A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 880 through 903 removed outlier: 3.844A pdb=" N LEU B 884 " --> pdb=" O GLU B 880 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 893 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL B 898 " --> pdb=" O VAL B 894 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.539A pdb=" N LEU B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 939 No H-bonds generated for 'chain 'B' and resid 937 through 939' Processing helix chain 'B' and resid 940 through 945 Processing helix chain 'B' and resid 954 through 962 removed outlier: 4.697A pdb=" N LYS B 960 " --> pdb=" O PRO B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 975 through 990 removed outlier: 4.221A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1002 removed outlier: 3.632A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B1000 " --> pdb=" O TYR B 996 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 15 removed outlier: 5.990A pdb=" N ARG A 15 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 21 " --> pdb=" O ARG A 15 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 63 current: chain 'A' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 191 through 195 current: chain 'A' and resid 219 through 222 Processing sheet with id=AA2, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 15 removed outlier: 6.684A pdb=" N VAL D 11 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR D 24 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE D 13 " --> pdb=" O VAL D 22 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 63 current: chain 'D' and resid 192 through 200 Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 642 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3001 1.33 - 1.45: 3186 1.45 - 1.57: 7431 1.57 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 13706 Sorted by residual: bond pdb=" CA ARG A 15 " pdb=" C ARG A 15 " ideal model delta sigma weight residual 1.523 1.452 0.071 1.28e-02 6.10e+03 3.08e+01 bond pdb=" N LYS A 16 " pdb=" CA LYS A 16 " ideal model delta sigma weight residual 1.457 1.402 0.055 1.29e-02 6.01e+03 1.84e+01 bond pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" CA SER C 855 " pdb=" C SER C 855 " ideal model delta sigma weight residual 1.525 1.485 0.041 1.29e-02 6.01e+03 9.86e+00 bond pdb=" CA LEU C 854 " pdb=" CB LEU C 854 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.53e-02 4.27e+03 8.68e+00 ... (remaining 13701 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.74: 122 105.74 - 112.82: 6881 112.82 - 119.89: 4852 119.89 - 126.97: 6495 126.97 - 134.05: 81 Bond angle restraints: 18431 Sorted by residual: angle pdb=" N LYS A 16 " pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 110.80 98.67 12.13 2.13e+00 2.20e-01 3.25e+01 angle pdb=" N SER C 855 " pdb=" CA SER C 855 " pdb=" C SER C 855 " ideal model delta sigma weight residual 112.04 104.35 7.69 1.44e+00 4.82e-01 2.85e+01 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 110.44 104.81 5.63 1.20e+00 6.94e-01 2.20e+01 angle pdb=" CA GLU B 880 " pdb=" CB GLU B 880 " pdb=" CG GLU B 880 " ideal model delta sigma weight residual 114.10 122.37 -8.27 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CA GLU C 880 " pdb=" CB GLU C 880 " pdb=" CG GLU C 880 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 18426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6769 17.95 - 35.89: 993 35.89 - 53.84: 311 53.84 - 71.79: 59 71.79 - 89.73: 29 Dihedral angle restraints: 8161 sinusoidal: 3364 harmonic: 4797 Sorted by residual: dihedral pdb=" CA LYS B 953 " pdb=" C LYS B 953 " pdb=" N PHE B 954 " pdb=" CA PHE B 954 " ideal model delta harmonic sigma weight residual 180.00 157.34 22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LYS C 953 " pdb=" C LYS C 953 " pdb=" N PHE C 954 " pdb=" CA PHE C 954 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA THR B 906 " pdb=" C THR B 906 " pdb=" N PHE B 907 " pdb=" CA PHE B 907 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 8158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1617 0.053 - 0.106: 308 0.106 - 0.159: 28 0.159 - 0.212: 3 0.212 - 0.265: 4 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CG LEU B 959 " pdb=" CB LEU B 959 " pdb=" CD1 LEU B 959 " pdb=" CD2 LEU B 959 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU C 959 " pdb=" CB LEU C 959 " pdb=" CD1 LEU C 959 " pdb=" CD2 LEU C 959 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE B 515 " pdb=" CA ILE B 515 " pdb=" CG1 ILE B 515 " pdb=" CG2 ILE B 515 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1957 not shown) Planarity restraints: 2353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 878 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO C 879 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 879 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 879 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 343 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ASN B 343 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN B 343 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 344 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 878 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 879 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 879 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 879 " 0.030 5.00e-02 4.00e+02 ... (remaining 2350 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 554 2.72 - 3.27: 13240 3.27 - 3.81: 21208 3.81 - 4.36: 25758 4.36 - 4.90: 44442 Nonbonded interactions: 105202 Sorted by model distance: nonbonded pdb=" OG SER C 429 " pdb=" OD1 ASP C 435 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 429 " pdb=" OD1 ASP B 435 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP D 225 " pdb=" OG1 THR D 228 " model vdw 2.192 3.040 nonbonded pdb=" OH TYR C 709 " pdb=" OD2 ASP C 748 " model vdw 2.198 3.040 nonbonded pdb=" O SER A 201 " pdb=" OG SER A 201 " model vdw 2.237 3.040 ... (remaining 105197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 33 or resid 52 through 177 or resid 190 through \ 211 or resid 216 through 236)) selection = (chain 'D' and (resid 5 through 74 or resid 168 through 227 or (resid 228 throug \ h 229 and (name N or name CA or name C or name O or name CB )) or resid 230 thro \ ugh 235 or (resid 236 and (name N or name CA or name C or name O or name CB )))) \ } ncs_group { reference = (chain 'B' and (resid 304 through 638 or (resid 639 and (name N or name CA or na \ me C or name O or name CB )) or resid 640 or resid 643 through 932 or (resid 933 \ and (name N or name CA or name C or name O or name CB )) or resid 934 through 1 \ 005)) selection = (chain 'C' and (resid 304 through 349 or resid 354 through 1005)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.130 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13706 Z= 0.180 Angle : 0.581 12.134 18431 Z= 0.313 Chirality : 0.041 0.265 1960 Planarity : 0.003 0.057 2353 Dihedral : 19.216 89.734 5065 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.77 % Rotamer: Outliers : 3.15 % Allowed : 33.06 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1589 helix: 0.73 (0.18), residues: 899 sheet: 1.25 (0.55), residues: 99 loop : -1.64 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 958 HIS 0.011 0.001 HIS C 349 PHE 0.031 0.001 PHE C 354 TYR 0.023 0.001 TYR B 356 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.600 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: B 320 PHE cc_start: 0.6420 (m-80) cc_final: 0.5455 (t80) REVERT: B 495 LEU cc_start: 0.6465 (tm) cc_final: 0.6261 (tp) outliers start: 46 outliers final: 40 residues processed: 213 average time/residue: 0.8854 time to fit residues: 213.7989 Evaluate side-chains 211 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 476 ILE Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 845 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 951 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 475 GLN C 591 ASN ** C 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 ASN B 349 HIS B 591 ASN B 606 HIS B 867 ASN B 910 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13706 Z= 0.338 Angle : 0.641 8.685 18431 Z= 0.349 Chirality : 0.046 0.345 1960 Planarity : 0.004 0.054 2353 Dihedral : 7.305 58.895 1833 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.67 % Favored : 93.20 % Rotamer: Outliers : 7.87 % Allowed : 27.31 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1589 helix: 0.20 (0.17), residues: 916 sheet: 0.74 (0.52), residues: 102 loop : -1.90 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 958 HIS 0.009 0.002 HIS B 349 PHE 0.023 0.002 PHE B 387 TYR 0.024 0.002 TYR B 472 ARG 0.003 0.001 ARG C 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 178 time to evaluate : 1.523 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: C 730 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5696 (mt-10) REVERT: C 877 PHE cc_start: 0.5850 (OUTLIER) cc_final: 0.4653 (m-80) REVERT: C 976 MET cc_start: 0.3642 (OUTLIER) cc_final: 0.2729 (ppp) REVERT: D 28 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: B 320 PHE cc_start: 0.6655 (m-80) cc_final: 0.6341 (m-80) REVERT: B 497 LEU cc_start: 0.7872 (mt) cc_final: 0.7649 (mt) REVERT: B 730 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5676 (mt-10) REVERT: B 760 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6900 (ptp-110) REVERT: B 877 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.4784 (m-80) REVERT: B 936 MET cc_start: 0.5328 (tmm) cc_final: 0.5094 (tmm) REVERT: B 976 MET cc_start: 0.3560 (OUTLIER) cc_final: 0.2556 (ppp) outliers start: 115 outliers final: 41 residues processed: 271 average time/residue: 0.9034 time to fit residues: 275.7048 Evaluate side-chains 220 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 171 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 954 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 MET Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 475 GLN B 349 HIS B 467 ASN B 475 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13706 Z= 0.221 Angle : 0.569 8.629 18431 Z= 0.309 Chirality : 0.042 0.317 1960 Planarity : 0.004 0.054 2353 Dihedral : 6.074 58.703 1789 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 6.02 % Allowed : 29.64 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1589 helix: 0.40 (0.17), residues: 919 sheet: 0.65 (0.53), residues: 97 loop : -1.82 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 601 HIS 0.010 0.001 HIS C 349 PHE 0.024 0.002 PHE B 387 TYR 0.016 0.002 TYR C 472 ARG 0.002 0.000 ARG C 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 180 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 730 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5572 (mt-10) REVERT: C 767 LEU cc_start: 0.7524 (tp) cc_final: 0.7012 (tt) REVERT: C 877 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.4609 (m-80) REVERT: B 730 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5533 (mt-10) REVERT: B 760 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6911 (ptp-110) REVERT: B 877 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: B 930 MET cc_start: 0.6407 (mmm) cc_final: 0.6070 (mmm) REVERT: B 936 MET cc_start: 0.5364 (tmm) cc_final: 0.5027 (tmm) REVERT: B 976 MET cc_start: 0.3420 (OUTLIER) cc_final: 0.2533 (ppp) outliers start: 88 outliers final: 36 residues processed: 250 average time/residue: 0.8982 time to fit residues: 253.3294 Evaluate side-chains 210 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 914 SER Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 907 PHE Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 933 PHE Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS B 349 HIS B 467 ASN B 867 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13706 Z= 0.167 Angle : 0.544 9.369 18431 Z= 0.292 Chirality : 0.041 0.346 1960 Planarity : 0.003 0.055 2353 Dihedral : 5.217 56.393 1778 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 5.95 % Allowed : 29.64 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1589 helix: 0.67 (0.17), residues: 911 sheet: 0.75 (0.54), residues: 98 loop : -1.68 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 601 HIS 0.010 0.001 HIS C 349 PHE 0.024 0.001 PHE B 387 TYR 0.018 0.001 TYR B 539 ARG 0.002 0.000 ARG A 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 180 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 LEU cc_start: 0.6537 (mp) cc_final: 0.6320 (mp) REVERT: C 626 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: C 730 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5531 (mt-10) REVERT: C 767 LEU cc_start: 0.7297 (tp) cc_final: 0.6801 (tt) REVERT: C 877 PHE cc_start: 0.5769 (OUTLIER) cc_final: 0.4573 (m-80) REVERT: B 531 MET cc_start: 0.6627 (mtm) cc_final: 0.6270 (mtm) REVERT: B 730 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.5512 (mt-10) REVERT: B 760 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6851 (ptp-110) REVERT: B 877 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.4659 (m-80) REVERT: B 936 MET cc_start: 0.5518 (tmm) cc_final: 0.5158 (tmm) outliers start: 87 outliers final: 32 residues processed: 252 average time/residue: 0.8995 time to fit residues: 257.0733 Evaluate side-chains 210 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 639 PHE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 940 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 115 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 475 GLN ** C 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN B 867 ASN B 978 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13706 Z= 0.212 Angle : 0.567 9.777 18431 Z= 0.304 Chirality : 0.042 0.379 1960 Planarity : 0.004 0.054 2353 Dihedral : 4.971 53.135 1771 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 6.37 % Allowed : 29.91 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1589 helix: 0.64 (0.17), residues: 909 sheet: 0.62 (0.53), residues: 98 loop : -1.73 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 601 HIS 0.013 0.002 HIS C 978 PHE 0.024 0.002 PHE B 387 TYR 0.015 0.002 TYR C 472 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 182 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 319 LEU cc_start: 0.6349 (mp) cc_final: 0.6103 (mp) REVERT: C 343 ASN cc_start: 0.7227 (p0) cc_final: 0.6282 (t0) REVERT: C 425 ILE cc_start: 0.5949 (OUTLIER) cc_final: 0.5742 (mm) REVERT: C 626 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: C 730 GLU cc_start: 0.5965 (OUTLIER) cc_final: 0.5578 (mt-10) REVERT: C 767 LEU cc_start: 0.7336 (tp) cc_final: 0.6920 (tt) REVERT: C 851 SER cc_start: 0.4820 (OUTLIER) cc_final: 0.4490 (m) REVERT: C 877 PHE cc_start: 0.5840 (OUTLIER) cc_final: 0.4661 (m-80) REVERT: D 28 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: B 531 MET cc_start: 0.6727 (mtm) cc_final: 0.6431 (mtm) REVERT: B 730 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5567 (mt-10) REVERT: B 760 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.6831 (ptp-110) REVERT: B 877 PHE cc_start: 0.5842 (OUTLIER) cc_final: 0.4749 (m-80) REVERT: B 913 MET cc_start: 0.7333 (ttt) cc_final: 0.6992 (ttt) REVERT: B 930 MET cc_start: 0.6344 (mmm) cc_final: 0.5977 (mmm) REVERT: B 936 MET cc_start: 0.5499 (tmm) cc_final: 0.5183 (tmm) outliers start: 93 outliers final: 44 residues processed: 256 average time/residue: 0.8479 time to fit residues: 246.4340 Evaluate side-chains 226 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 30 optimal weight: 0.0770 chunk 90 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 978 HIS D 194 GLN B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13706 Z= 0.208 Angle : 0.571 10.575 18431 Z= 0.306 Chirality : 0.042 0.388 1960 Planarity : 0.004 0.055 2353 Dihedral : 4.811 51.015 1768 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 5.54 % Allowed : 31.07 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1589 helix: 0.68 (0.17), residues: 909 sheet: 0.64 (0.53), residues: 98 loop : -1.73 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 601 HIS 0.019 0.002 HIS B 978 PHE 0.025 0.001 PHE B 387 TYR 0.017 0.002 TYR B 539 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 177 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 ASN cc_start: 0.7209 (p0) cc_final: 0.6259 (t0) REVERT: C 626 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: C 730 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5576 (mt-10) REVERT: C 767 LEU cc_start: 0.7261 (tp) cc_final: 0.6826 (tt) REVERT: C 851 SER cc_start: 0.4773 (OUTLIER) cc_final: 0.4473 (m) REVERT: C 877 PHE cc_start: 0.5824 (OUTLIER) cc_final: 0.4614 (m-80) REVERT: D 26 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: D 28 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7952 (tt0) REVERT: B 320 PHE cc_start: 0.6618 (m-80) cc_final: 0.5528 (t80) REVERT: B 349 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6293 (t-90) REVERT: B 531 MET cc_start: 0.6602 (mtm) cc_final: 0.6399 (mtm) REVERT: B 730 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5567 (mt-10) REVERT: B 760 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6824 (ptp-110) REVERT: B 877 PHE cc_start: 0.5872 (OUTLIER) cc_final: 0.4774 (m-80) outliers start: 81 outliers final: 45 residues processed: 242 average time/residue: 0.8378 time to fit residues: 230.0392 Evaluate side-chains 226 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 171 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 88 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 867 ASN C 978 HIS B 349 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13706 Z= 0.194 Angle : 0.572 11.297 18431 Z= 0.305 Chirality : 0.043 0.396 1960 Planarity : 0.004 0.055 2353 Dihedral : 4.769 48.583 1768 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.23 % Favored : 93.64 % Rotamer: Outliers : 5.61 % Allowed : 31.35 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1589 helix: 0.73 (0.17), residues: 910 sheet: 0.67 (0.54), residues: 98 loop : -1.72 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 601 HIS 0.019 0.002 HIS C 978 PHE 0.025 0.001 PHE B 387 TYR 0.016 0.002 TYR C 472 ARG 0.003 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 178 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 320 PHE cc_start: 0.6680 (m-80) cc_final: 0.6475 (m-80) REVERT: C 343 ASN cc_start: 0.7169 (p0) cc_final: 0.6261 (t0) REVERT: C 730 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5548 (mt-10) REVERT: C 767 LEU cc_start: 0.7258 (tp) cc_final: 0.6823 (tt) REVERT: C 851 SER cc_start: 0.4780 (OUTLIER) cc_final: 0.4508 (m) REVERT: C 877 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.4591 (m-80) REVERT: C 913 MET cc_start: 0.7336 (ttt) cc_final: 0.7023 (ttt) REVERT: D 26 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: D 28 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: B 320 PHE cc_start: 0.6668 (m-80) cc_final: 0.5588 (t80) REVERT: B 730 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5538 (mt-10) REVERT: B 760 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6810 (ptp-110) REVERT: B 851 SER cc_start: 0.4813 (OUTLIER) cc_final: 0.4508 (m) REVERT: B 877 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.4807 (m-80) outliers start: 82 outliers final: 44 residues processed: 243 average time/residue: 0.9067 time to fit residues: 248.9929 Evaluate side-chains 226 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 770 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 997 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 978 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13706 Z= 0.276 Angle : 0.617 11.139 18431 Z= 0.329 Chirality : 0.044 0.429 1960 Planarity : 0.004 0.054 2353 Dihedral : 5.003 50.035 1768 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 5.68 % Allowed : 30.87 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1589 helix: 0.52 (0.17), residues: 909 sheet: 0.55 (0.53), residues: 98 loop : -1.78 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 958 HIS 0.019 0.002 HIS C 978 PHE 0.029 0.002 PHE C 354 TYR 0.023 0.002 TYR C 356 ARG 0.004 0.000 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 172 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: C 343 ASN cc_start: 0.7237 (p0) cc_final: 0.6312 (t0) REVERT: C 349 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6162 (t-90) REVERT: C 730 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5647 (mt-10) REVERT: C 772 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7330 (mp) REVERT: C 851 SER cc_start: 0.4839 (OUTLIER) cc_final: 0.4510 (m) REVERT: C 877 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.4591 (m-80) REVERT: C 913 MET cc_start: 0.7395 (ttt) cc_final: 0.7080 (ttt) REVERT: D 26 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7276 (pt0) REVERT: D 28 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: B 320 PHE cc_start: 0.6663 (m-80) cc_final: 0.5565 (t80) REVERT: B 730 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5604 (mt-10) REVERT: B 760 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.6792 (ptp-110) REVERT: B 840 LYS cc_start: 0.4634 (mmtt) cc_final: 0.4378 (mmmt) REVERT: B 851 SER cc_start: 0.4732 (OUTLIER) cc_final: 0.4359 (m) REVERT: B 877 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.4788 (m-80) outliers start: 83 outliers final: 45 residues processed: 238 average time/residue: 0.8611 time to fit residues: 232.7870 Evaluate side-chains 226 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 169 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 579 SER Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 770 SER Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 921 PHE Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 940 TYR Chi-restraints excluded: chain B residue 978 HIS Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1000 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS C 978 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13706 Z= 0.173 Angle : 0.581 12.373 18431 Z= 0.309 Chirality : 0.042 0.398 1960 Planarity : 0.004 0.056 2353 Dihedral : 4.760 45.628 1768 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 3.63 % Allowed : 33.06 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1589 helix: 0.75 (0.17), residues: 912 sheet: 0.72 (0.55), residues: 98 loop : -1.69 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 601 HIS 0.017 0.002 HIS B 978 PHE 0.025 0.001 PHE B 387 TYR 0.018 0.002 TYR C 356 ARG 0.005 0.000 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 172 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 ASN cc_start: 0.7186 (p0) cc_final: 0.6269 (t0) REVERT: C 730 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5511 (mt-10) REVERT: C 772 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7345 (mp) REVERT: C 851 SER cc_start: 0.4794 (OUTLIER) cc_final: 0.4550 (m) REVERT: C 877 PHE cc_start: 0.5807 (OUTLIER) cc_final: 0.4606 (m-80) REVERT: D 26 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: D 28 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: B 320 PHE cc_start: 0.6590 (m-80) cc_final: 0.5583 (t80) REVERT: B 730 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5525 (mt-10) REVERT: B 760 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6796 (ptp-110) REVERT: B 840 LYS cc_start: 0.4625 (mmtt) cc_final: 0.4251 (mmmt) REVERT: B 851 SER cc_start: 0.4795 (OUTLIER) cc_final: 0.4504 (m) REVERT: B 877 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.4797 (m-80) outliers start: 53 outliers final: 30 residues processed: 217 average time/residue: 0.8955 time to fit residues: 219.4803 Evaluate side-chains 209 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 169 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 756 VAL Chi-restraints excluded: chain C residue 772 ILE Chi-restraints excluded: chain C residue 851 SER Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 978 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 0.0370 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13706 Z= 0.177 Angle : 0.583 12.549 18431 Z= 0.308 Chirality : 0.043 0.410 1960 Planarity : 0.004 0.056 2353 Dihedral : 4.678 41.867 1768 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 3.42 % Allowed : 33.54 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1589 helix: 0.80 (0.17), residues: 912 sheet: 0.80 (0.55), residues: 98 loop : -1.67 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 601 HIS 0.020 0.002 HIS B 978 PHE 0.030 0.001 PHE C 354 TYR 0.018 0.002 TYR C 356 ARG 0.003 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3178 Ramachandran restraints generated. 1589 Oldfield, 0 Emsley, 1589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 180 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 ASN cc_start: 0.7194 (p0) cc_final: 0.6298 (t0) REVERT: C 730 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.5508 (mt-10) REVERT: C 772 ILE cc_start: 0.7524 (mt) cc_final: 0.7296 (mp) REVERT: C 877 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: D 26 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7233 (pt0) REVERT: D 28 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 320 PHE cc_start: 0.6533 (m-80) cc_final: 0.5573 (t80) REVERT: B 730 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.5521 (mt-10) REVERT: B 760 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6744 (ptp-110) REVERT: B 840 LYS cc_start: 0.4645 (mmtt) cc_final: 0.4264 (mmmt) REVERT: B 851 SER cc_start: 0.4712 (OUTLIER) cc_final: 0.4433 (m) REVERT: B 877 PHE cc_start: 0.5929 (OUTLIER) cc_final: 0.4827 (m-80) REVERT: B 905 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6435 (tm-30) outliers start: 50 outliers final: 30 residues processed: 224 average time/residue: 0.8945 time to fit residues: 225.8000 Evaluate side-chains 208 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain C residue 329 ASP Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 691 ILE Chi-restraints excluded: chain C residue 730 GLU Chi-restraints excluded: chain C residue 877 PHE Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 927 ASN Chi-restraints excluded: chain C residue 978 HIS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 28 GLN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 730 GLU Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 828 THR Chi-restraints excluded: chain B residue 851 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 905 GLN Chi-restraints excluded: chain B residue 921 PHE Chi-restraints excluded: chain B residue 978 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 978 HIS D 194 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 ASN B 978 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.224866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195250 restraints weight = 16710.502| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.99 r_work: 0.4075 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13706 Z= 0.300 Angle : 0.648 11.603 18431 Z= 0.344 Chirality : 0.045 0.451 1960 Planarity : 0.004 0.053 2353 Dihedral : 5.034 46.348 1768 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 4.04 % Allowed : 32.92 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1589 helix: 0.50 (0.17), residues: 909 sheet: 0.53 (0.54), residues: 98 loop : -1.80 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 958 HIS 0.020 0.002 HIS C 978 PHE 0.028 0.002 PHE C 943 TYR 0.024 0.002 TYR C 356 ARG 0.007 0.000 ARG D 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4562.94 seconds wall clock time: 80 minutes 44.60 seconds (4844.60 seconds total)