Starting phenix.real_space_refine on Fri Mar 15 12:52:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kft_22855/03_2024/7kft_22855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kft_22855/03_2024/7kft_22855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kft_22855/03_2024/7kft_22855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kft_22855/03_2024/7kft_22855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kft_22855/03_2024/7kft_22855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kft_22855/03_2024/7kft_22855.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 25 5.16 5 C 7433 2.51 5 N 2135 2.21 5 O 2087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D ASP 666": "OD1" <-> "OD2" Residue "D GLU 708": "OE1" <-> "OE2" Residue "D TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 763": "NH1" <-> "NH2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D GLU 814": "OE1" <-> "OE2" Residue "D ARG 834": "NH1" <-> "NH2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ASP 857": "OD1" <-> "OD2" Residue "D ASP 885": "OD1" <-> "OD2" Residue "D GLU 888": "OE1" <-> "OE2" Residue "D TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 913": "NH1" <-> "NH2" Residue "D ASP 917": "OD1" <-> "OD2" Residue "D ASP 922": "OD1" <-> "OD2" Residue "D ARG 931": "NH1" <-> "NH2" Residue "D TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 292": "NH1" <-> "NH2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ASP 350": "OD1" <-> "OD2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 455": "OE1" <-> "OE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C ASP 495": "OD1" <-> "OD2" Residue "C ASP 523": "OD1" <-> "OD2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 541": "OD1" <-> "OD2" Residue "C GLU 565": "OE1" <-> "OE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "E ASP 666": "OD1" <-> "OD2" Residue "E ASP 675": "OD1" <-> "OD2" Residue "E GLU 685": "OE1" <-> "OE2" Residue "E TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 774": "NH1" <-> "NH2" Residue "E ARG 801": "NH1" <-> "NH2" Residue "E ARG 834": "NH1" <-> "NH2" Residue "E ASP 839": "OD1" <-> "OD2" Residue "E PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 891": "NH1" <-> "NH2" Residue "E ASP 911": "OD1" <-> "OD2" Residue "E ARG 913": "NH1" <-> "NH2" Residue "E ASP 917": "OD1" <-> "OD2" Residue "E ARG 932": "NH1" <-> "NH2" Residue "E PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11680 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "A" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 756 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "D" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "C" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4601 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 25, 'TRANS': 542} Chain breaks: 5 Chain: "E" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2800 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 8, 'TRANS': 332} Time building chain proxies: 6.16, per 1000 atoms: 0.53 Number of scatterers: 11680 At special positions: 0 Unit cell: (87.838, 142.44, 122.261, 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 25 16.00 O 2087 8.00 N 2135 7.00 C 7433 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: 3.91 Conformation dependent library (CDL) restraints added in 2.1 seconds 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 48.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 removed outlier: 3.662A pdb=" N LYS B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.510A pdb=" N ILE B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.831A pdb=" N LYS A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.952A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 709 Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 748 through 773 removed outlier: 3.709A pdb=" N VAL D 760 " --> pdb=" O ALA D 756 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 771 " --> pdb=" O GLN D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR D 784 " --> pdb=" O GLN D 780 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 817 removed outlier: 3.525A pdb=" N LEU D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 822 Processing helix chain 'D' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 891 through 904 removed outlier: 3.816A pdb=" N GLU D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 927 through 944 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'C' and resid 28 through 41 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 150 removed outlier: 4.004A pdb=" N TRP C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.510A pdb=" N LEU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.542A pdb=" N CYS C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 370 removed outlier: 3.782A pdb=" N THR C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 430 through 445 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.647A pdb=" N ASP C 456 " --> pdb=" O ASP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.799A pdb=" N LEU C 466 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.371A pdb=" N LEU C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 523 removed outlier: 3.546A pdb=" N ASP C 523 " --> pdb=" O ILE C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 620 through 628 removed outlier: 4.118A pdb=" N ALA C 624 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 709 Processing helix chain 'E' and resid 736 through 746 Processing helix chain 'E' and resid 748 through 771 Processing helix chain 'E' and resid 772 through 773 No H-bonds generated for 'chain 'E' and resid 772 through 773' Processing helix chain 'E' and resid 774 through 780 removed outlier: 3.538A pdb=" N HIS E 777 " --> pdb=" O ARG E 774 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS E 779 " --> pdb=" O ALA E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 796 removed outlier: 3.635A pdb=" N LEU E 785 " --> pdb=" O LEU E 781 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 796 " --> pdb=" O GLN E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 817 removed outlier: 4.509A pdb=" N ASN E 805 " --> pdb=" O ARG E 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 806 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 828 removed outlier: 3.738A pdb=" N HIS E 828 " --> pdb=" O GLU E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 864 removed outlier: 3.699A pdb=" N VAL E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU E 844 " --> pdb=" O PRO E 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 845 " --> pdb=" O PHE E 841 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR E 850 " --> pdb=" O SER E 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 851 " --> pdb=" O LEU E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 887 Processing helix chain 'E' and resid 896 through 904 Processing helix chain 'E' and resid 927 through 944 Processing helix chain 'E' and resid 951 through 968 removed outlier: 4.033A pdb=" N GLN E 957 " --> pdb=" O GLN E 953 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.255A pdb=" N HIS B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.503A pdb=" N HIS B 80 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 31 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU A 36 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG A 29 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 652 through 656 removed outlier: 5.724A pdb=" N THR D 652 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 689 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N HIS D 714 " --> pdb=" O HIS D 688 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 690 " --> pdb=" O HIS D 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 716 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 692 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY D 724 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 727 " --> pdb=" O ALA D 725 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 724 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 713 " --> pdb=" O VAL E 726 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR E 652 " --> pdb=" O HIS E 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 690 " --> pdb=" O THR E 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 654 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 692 " --> pdb=" O LEU E 654 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU E 656 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 674 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 912 through 916 Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE C 236 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 268 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS C 238 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY C 263 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 161 " --> pdb=" O LYS C 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.509A pdb=" N HIS C 492 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 580 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 533 through 538 removed outlier: 4.112A pdb=" N ILE C 544 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL E 672 " --> pdb=" O THR E 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 681 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU E 670 " --> pdb=" O LYS E 681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 912 through 916 544 hydrogen bonds defined for protein. 1551 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: 3.60 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3866 1.34 - 1.46: 1824 1.46 - 1.57: 6203 1.57 - 1.69: 1 1.69 - 1.81: 43 Bond restraints: 11937 Sorted by residual: bond pdb=" CB VAL E 713 " pdb=" CG1 VAL E 713 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.23e+00 bond pdb=" CB LYS C 346 " pdb=" CG LYS C 346 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.32e+00 bond pdb=" CB VAL E 690 " pdb=" CG1 VAL E 690 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.28e+00 bond pdb=" N LYS C 307 " pdb=" CA LYS C 307 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.97e+00 bond pdb=" CB ASP C 540 " pdb=" CG ASP C 540 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.81e+00 ... (remaining 11932 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.46: 185 105.46 - 112.62: 6248 112.62 - 119.78: 3968 119.78 - 126.94: 5542 126.94 - 134.10: 178 Bond angle restraints: 16121 Sorted by residual: angle pdb=" C ASP D 666 " pdb=" N ASN D 667 " pdb=" CA ASN D 667 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C GLU E 979 " pdb=" N LEU E 980 " pdb=" CA LEU E 980 " ideal model delta sigma weight residual 120.82 126.55 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" N LEU E 919 " pdb=" CA LEU E 919 " pdb=" C LEU E 919 " ideal model delta sigma weight residual 114.75 109.95 4.80 1.26e+00 6.30e-01 1.45e+01 angle pdb=" CA GLN C 232 " pdb=" CB GLN C 232 " pdb=" CG GLN C 232 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C ALA D 877 " pdb=" N ALA D 878 " pdb=" CA ALA D 878 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 ... (remaining 16116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6425 17.86 - 35.73: 648 35.73 - 53.59: 104 53.59 - 71.45: 22 71.45 - 89.32: 4 Dihedral angle restraints: 7203 sinusoidal: 3012 harmonic: 4191 Sorted by residual: dihedral pdb=" CA ARG E 891 " pdb=" C ARG E 891 " pdb=" N HIS E 892 " pdb=" CA HIS E 892 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N PRO D 836 " pdb=" CA PRO D 836 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASP E 917 " pdb=" C ASP E 917 " pdb=" N HIS E 918 " pdb=" CA HIS E 918 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 7200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1458 0.065 - 0.130: 280 0.130 - 0.194: 26 0.194 - 0.259: 1 0.259 - 0.324: 1 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CB ILE A 66 " pdb=" CA ILE A 66 " pdb=" CG1 ILE A 66 " pdb=" CG2 ILE A 66 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1763 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 41 " -0.044 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO A 42 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 477 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO C 478 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 346 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C LYS C 346 " -0.039 2.00e-02 2.50e+03 pdb=" O LYS C 346 " 0.015 2.00e-02 2.50e+03 pdb=" N THR C 347 " 0.013 2.00e-02 2.50e+03 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2085 2.77 - 3.30: 10599 3.30 - 3.83: 17653 3.83 - 4.37: 20562 4.37 - 4.90: 37055 Nonbonded interactions: 87954 Sorted by model distance: nonbonded pdb=" OD1 ASP C 415 " pdb=" OH TYR C 425 " model vdw 2.237 2.440 nonbonded pdb=" NE2 HIS E 714 " pdb=" OD2 ASP E 857 " model vdw 2.246 2.520 nonbonded pdb=" O GLN E 906 " pdb=" NH2 ARG E 933 " model vdw 2.277 2.520 nonbonded pdb=" OH TYR D 815 " pdb=" OE1 GLU D 895 " model vdw 2.283 2.440 nonbonded pdb=" NE ARG B 44 " pdb=" OE2 GLU E 685 " model vdw 2.293 2.520 ... (remaining 87949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 90) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 650 through 981) } 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: 5.950 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: 14.220 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 31.300 Find NCS groups from input model: 0.500 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.005 0.075 11937 Z= 0.364 Angle : 0.831 8.936 16121 Z= 0.471 Chirality : 0.050 0.324 1766 Planarity : 0.005 0.068 2069 Dihedral : 14.402 89.317 4483 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.99 (0.21), residues: 1407 helix: 0.28 (0.20), residues: 631 sheet: -0.06 (0.41), residues: 162 loop : -1.82 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 162 HIS 0.009 0.001 HIS A 53 PHE 0.020 0.002 PHE D 819 TYR 0.021 0.002 TYR D 815 ARG 0.028 0.001 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.226 Fit side-chains REVERT: A 48 LEU cc_start: 0.7020 (tt) cc_final: 0.6482 (mp) REVERT: C 355 ARG cc_start: 0.5808 (tpt-90) cc_final: 0.5605 (ttp80) REVERT: C 368 ARG cc_start: 0.8100 (tmt170) cc_final: 0.7575 (ttm170) REVERT: E 779 LYS cc_start: 0.7532 (tmtt) cc_final: 0.7174 (tppt) REVERT: E 834 ARG cc_start: 0.8072 (ttm110) cc_final: 0.7760 (ttm110) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2503 time to fit residues: 50.6790 Evaluate side-chains 119 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN D 842 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11937 Z= 0.230 Angle : 0.583 7.591 16121 Z= 0.307 Chirality : 0.044 0.176 1766 Planarity : 0.005 0.063 2069 Dihedral : 4.903 20.913 1554 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.11 % Allowed : 5.86 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1407 helix: 0.95 (0.21), residues: 644 sheet: 0.49 (0.43), residues: 146 loop : -1.73 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 162 HIS 0.006 0.001 HIS C 91 PHE 0.018 0.002 PHE C 70 TYR 0.013 0.001 TYR D 815 ARG 0.006 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: D 686 GLN cc_start: 0.8039 (mt0) cc_final: 0.7809 (mp10) REVERT: C 80 GLN cc_start: 0.7967 (pp30) cc_final: 0.7685 (pp30) REVERT: C 368 ARG cc_start: 0.8062 (tmt170) cc_final: 0.7715 (ttm-80) REVERT: C 560 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7511 (tm-30) REVERT: E 779 LYS cc_start: 0.7684 (tmtt) cc_final: 0.7292 (tppt) outliers start: 14 outliers final: 13 residues processed: 130 average time/residue: 0.2644 time to fit residues: 48.4812 Evaluate side-chains 133 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 919 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 842 ASN C 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11937 Z= 0.190 Angle : 0.535 7.171 16121 Z= 0.281 Chirality : 0.043 0.151 1766 Planarity : 0.004 0.066 2069 Dihedral : 4.627 20.906 1554 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.43 % Allowed : 8.08 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1407 helix: 1.34 (0.21), residues: 640 sheet: 0.56 (0.42), residues: 154 loop : -1.61 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 162 HIS 0.005 0.001 HIS C 91 PHE 0.016 0.001 PHE C 70 TYR 0.012 0.001 TYR C 398 ARG 0.008 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.379 Fit side-chains REVERT: A 48 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6558 (mp) REVERT: C 30 MET cc_start: 0.7154 (mtm) cc_final: 0.5852 (mmp) REVERT: C 80 GLN cc_start: 0.7991 (pp30) cc_final: 0.7607 (pp30) REVERT: C 368 ARG cc_start: 0.8036 (tmt170) cc_final: 0.7762 (ttm-80) REVERT: C 560 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7483 (tm-30) REVERT: E 779 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7325 (tppt) outliers start: 18 outliers final: 13 residues processed: 138 average time/residue: 0.2579 time to fit residues: 50.8507 Evaluate side-chains 128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11937 Z= 0.215 Angle : 0.539 8.050 16121 Z= 0.281 Chirality : 0.043 0.155 1766 Planarity : 0.004 0.062 2069 Dihedral : 4.526 20.617 1554 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.98 % Allowed : 10.06 % Favored : 87.97 % 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 (0.23), residues: 1407 helix: 1.46 (0.21), residues: 640 sheet: 0.53 (0.42), residues: 154 loop : -1.59 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.004 0.001 HIS C 91 PHE 0.020 0.001 PHE C 70 TYR 0.012 0.001 TYR C 398 ARG 0.008 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.374 Fit side-chains REVERT: A 48 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6665 (mp) REVERT: D 938 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7956 (tp) REVERT: C 30 MET cc_start: 0.7165 (mtm) cc_final: 0.5849 (mmp) REVERT: C 80 GLN cc_start: 0.7963 (pp30) cc_final: 0.7477 (pp30) REVERT: C 368 ARG cc_start: 0.8039 (tmt170) cc_final: 0.7764 (ttm-80) REVERT: C 560 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7496 (tm-30) REVERT: E 779 LYS cc_start: 0.7652 (tmtt) cc_final: 0.7318 (tppt) outliers start: 25 outliers final: 17 residues processed: 134 average time/residue: 0.2567 time to fit residues: 49.1027 Evaluate side-chains 128 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11937 Z= 0.260 Angle : 0.559 6.982 16121 Z= 0.291 Chirality : 0.044 0.162 1766 Planarity : 0.004 0.061 2069 Dihedral : 4.556 20.599 1554 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.74 % Allowed : 11.80 % Favored : 86.46 % 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: 0.08 (0.23), residues: 1407 helix: 1.41 (0.21), residues: 640 sheet: 0.49 (0.42), residues: 153 loop : -1.59 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.005 0.001 HIS E 696 PHE 0.018 0.002 PHE C 70 TYR 0.015 0.002 TYR D 815 ARG 0.011 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.240 Fit side-chains REVERT: B 26 TYR cc_start: 0.8980 (m-80) cc_final: 0.8690 (m-80) REVERT: A 48 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6515 (mp) REVERT: C 80 GLN cc_start: 0.7897 (pp30) cc_final: 0.7334 (pp30) REVERT: C 368 ARG cc_start: 0.8055 (tmt170) cc_final: 0.7794 (ttm-80) REVERT: E 779 LYS cc_start: 0.7668 (tmtt) cc_final: 0.7417 (tppt) outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.2556 time to fit residues: 46.2298 Evaluate side-chains 126 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 738 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11937 Z= 0.206 Angle : 0.529 6.851 16121 Z= 0.276 Chirality : 0.043 0.159 1766 Planarity : 0.004 0.060 2069 Dihedral : 4.413 20.302 1554 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.90 % Allowed : 12.75 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1407 helix: 1.56 (0.21), residues: 642 sheet: 0.44 (0.42), residues: 154 loop : -1.52 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.003 0.001 HIS E 892 PHE 0.015 0.001 PHE C 70 TYR 0.012 0.001 TYR C 398 ARG 0.010 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.015 Fit side-chains REVERT: A 48 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6504 (mp) REVERT: A 72 ASN cc_start: 0.8341 (t0) cc_final: 0.7998 (t0) REVERT: C 30 MET cc_start: 0.7142 (mtm) cc_final: 0.5834 (mmp) REVERT: C 80 GLN cc_start: 0.7957 (pp30) cc_final: 0.7459 (pp30) REVERT: C 368 ARG cc_start: 0.8044 (tmt170) cc_final: 0.7790 (ttm-80) REVERT: E 779 LYS cc_start: 0.7720 (tmtt) cc_final: 0.7465 (tppt) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.2734 time to fit residues: 53.0606 Evaluate side-chains 134 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 chunk 62 optimal weight: 0.0770 chunk 84 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11937 Z= 0.154 Angle : 0.496 6.303 16121 Z= 0.259 Chirality : 0.041 0.155 1766 Planarity : 0.004 0.059 2069 Dihedral : 4.185 20.169 1554 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.58 % Allowed : 13.54 % Favored : 84.88 % 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: 0.52 (0.23), residues: 1407 helix: 1.87 (0.22), residues: 636 sheet: 0.49 (0.42), residues: 154 loop : -1.41 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.004 0.001 HIS E 952 PHE 0.014 0.001 PHE C 70 TYR 0.027 0.001 TYR C 210 ARG 0.012 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.389 Fit side-chains REVERT: A 47 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6771 (pp30) REVERT: A 48 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6221 (mp) REVERT: A 72 ASN cc_start: 0.8331 (t0) cc_final: 0.7952 (t0) REVERT: C 30 MET cc_start: 0.7086 (mtm) cc_final: 0.5827 (mmp) REVERT: C 80 GLN cc_start: 0.7930 (pp30) cc_final: 0.7543 (pp30) REVERT: C 368 ARG cc_start: 0.8024 (tmt170) cc_final: 0.7613 (ttm170) REVERT: E 779 LYS cc_start: 0.7722 (tmtt) cc_final: 0.7475 (tppt) REVERT: E 834 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7836 (ttm110) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.2619 time to fit residues: 52.0470 Evaluate side-chains 134 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11937 Z= 0.294 Angle : 0.560 6.350 16121 Z= 0.292 Chirality : 0.044 0.176 1766 Planarity : 0.004 0.059 2069 Dihedral : 4.394 20.587 1554 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.90 % Allowed : 14.25 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1407 helix: 1.56 (0.21), residues: 636 sheet: 0.29 (0.41), residues: 160 loop : -1.42 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 162 HIS 0.004 0.001 HIS C 172 PHE 0.015 0.002 PHE C 70 TYR 0.018 0.002 TYR C 210 ARG 0.010 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.515 Fit side-chains REVERT: A 48 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6724 (mp) REVERT: A 72 ASN cc_start: 0.8398 (t0) cc_final: 0.8030 (t0) REVERT: C 30 MET cc_start: 0.7150 (mtm) cc_final: 0.5854 (mmp) REVERT: C 80 GLN cc_start: 0.7983 (pp30) cc_final: 0.7549 (pp30) REVERT: C 368 ARG cc_start: 0.8079 (tmt170) cc_final: 0.7738 (ttm-80) REVERT: E 779 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7535 (tppt) outliers start: 24 outliers final: 18 residues processed: 135 average time/residue: 0.2564 time to fit residues: 50.0047 Evaluate side-chains 133 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 838 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11937 Z= 0.227 Angle : 0.536 7.123 16121 Z= 0.279 Chirality : 0.043 0.173 1766 Planarity : 0.004 0.060 2069 Dihedral : 4.369 20.425 1554 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.82 % Allowed : 14.57 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.23), residues: 1407 helix: 1.64 (0.21), residues: 636 sheet: 0.27 (0.42), residues: 160 loop : -1.40 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 162 HIS 0.003 0.001 HIS C 172 PHE 0.014 0.001 PHE C 70 TYR 0.019 0.001 TYR C 210 ARG 0.014 0.000 ARG E 834 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.331 Fit side-chains REVERT: A 47 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6762 (pp30) REVERT: A 48 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 72 ASN cc_start: 0.8363 (t0) cc_final: 0.7991 (t0) REVERT: C 30 MET cc_start: 0.7131 (mtm) cc_final: 0.5840 (mmp) REVERT: C 80 GLN cc_start: 0.7932 (pp30) cc_final: 0.7556 (pp30) REVERT: C 368 ARG cc_start: 0.8036 (tmt170) cc_final: 0.7773 (ttm-80) REVERT: C 442 TYR cc_start: 0.7189 (t80) cc_final: 0.6945 (t80) REVERT: E 779 LYS cc_start: 0.7836 (tmtt) cc_final: 0.7548 (tppt) REVERT: E 834 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7874 (ttm110) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.2484 time to fit residues: 46.1683 Evaluate side-chains 135 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 838 LYS Chi-restraints excluded: chain E residue 879 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 140 optimal weight: 0.0170 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 119 optimal weight: 0.0970 chunk 34 optimal weight: 0.0010 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 47 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 973 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11937 Z= 0.134 Angle : 0.501 7.904 16121 Z= 0.261 Chirality : 0.041 0.171 1766 Planarity : 0.004 0.061 2069 Dihedral : 4.164 20.022 1554 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.27 % Allowed : 15.12 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1407 helix: 2.02 (0.22), residues: 628 sheet: 0.30 (0.41), residues: 160 loop : -1.27 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 162 HIS 0.004 0.001 HIS E 952 PHE 0.012 0.001 PHE C 70 TYR 0.020 0.001 TYR C 210 ARG 0.013 0.000 ARG E 834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2814 Ramachandran restraints generated. 1407 Oldfield, 0 Emsley, 1407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.452 Fit side-chains REVERT: A 47 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6900 (pp30) REVERT: A 48 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6466 (mp) REVERT: A 72 ASN cc_start: 0.8355 (t0) cc_final: 0.7970 (t0) REVERT: C 80 GLN cc_start: 0.7888 (pp30) cc_final: 0.7600 (pp30) REVERT: C 368 ARG cc_start: 0.8045 (tmt170) cc_final: 0.7761 (ttm-80) REVERT: C 442 TYR cc_start: 0.6998 (t80) cc_final: 0.6777 (t80) REVERT: E 779 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7483 (tppt) REVERT: E 834 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7807 (ttm110) outliers start: 16 outliers final: 14 residues processed: 131 average time/residue: 0.2585 time to fit residues: 48.7103 Evaluate side-chains 133 residues out of total 1263 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain E residue 649 THR Chi-restraints excluded: chain E residue 664 THR Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 838 LYS Chi-restraints excluded: chain E residue 879 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.0040 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.160242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131855 restraints weight = 15092.620| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.28 r_work: 0.3471 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 11937 Z= 0.226 Angle : 0.791 59.199 16121 Z= 0.456 Chirality : 0.044 0.529 1766 Planarity : 0.004 0.061 2069 Dihedral : 4.162 20.034 1554 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.27 % Allowed : 15.20 % Favored : 83.53 % Cbeta Deviations : 0.07 % 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 (0.23), residues: 1407 helix: 1.91 (0.22), residues: 635 sheet: 0.31 (0.42), residues: 160 loop : -1.29 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 162 HIS 0.004 0.001 HIS E 952 PHE 0.013 0.001 PHE C 70 TYR 0.018 0.001 TYR C 210 ARG 0.012 0.000 ARG E 834 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.00 seconds wall clock time: 46 minutes 40.77 seconds (2800.77 seconds total)