Starting phenix.real_space_refine on Sat Mar 16 01:23:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/03_2024/7yg0_33803_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/03_2024/7yg0_33803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/03_2024/7yg0_33803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/03_2024/7yg0_33803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/03_2024/7yg0_33803_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/03_2024/7yg0_33803_neut.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 80 5.16 5 C 8685 2.51 5 N 2231 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A PHE 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A ASP 838": "OD1" <-> "OD2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 892": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 934": "NH1" <-> "NH2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ASP 943": "OD1" <-> "OD2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 968": "NH1" <-> "NH2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A TYR 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ASP 756": "OD1" <-> "OD2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 825": "OE1" <-> "OE2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B ASP 898": "OD1" <-> "OD2" Residue "B GLU 912": "OE1" <-> "OE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B GLU 1013": "OE1" <-> "OE2" Residue "B TYR 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13336 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6673 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 36, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 6663 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 36, 'TRANS': 817} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 7.07, per 1000 atoms: 0.53 Number of scatterers: 13336 At special positions: 0 Unit cell: (158.992, 84.726, 111.922, 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 80 16.00 O 2340 8.00 N 2231 7.00 C 8685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.04 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.04 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: 5.24 Conformation dependent library (CDL) restraints added in 2.3 seconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 2 sheets defined 63.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 158 through 194 removed outlier: 6.787A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 212 through 249 removed outlier: 3.718A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.600A pdb=" N ILE A 260 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 306 removed outlier: 3.548A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.644A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 351 No H-bonds generated for 'chain 'A' and resid 349 through 351' Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.211A pdb=" N GLY A 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 358 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 395 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.559A pdb=" N CYS A 421 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 453 through 486 removed outlier: 3.759A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.646A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 496 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS A 497 " --> pdb=" O PHE A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 524 through 553 Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 566 through 585 removed outlier: 3.629A pdb=" N THR A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 removed outlier: 3.611A pdb=" N ALA A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.878A pdb=" N ALA A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 655 through 665 removed outlier: 4.194A pdb=" N VAL A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 703 removed outlier: 4.686A pdb=" N GLN A 690 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 726 removed outlier: 3.518A pdb=" N LEU A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 removed outlier: 3.987A pdb=" N ASP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 5.315A pdb=" N PHE A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 823 " --> pdb=" O THR A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.507A pdb=" N THR A 843 " --> pdb=" O GLY A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.792A pdb=" N LYS A 858 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 884 removed outlier: 3.743A pdb=" N SER A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 4.274A pdb=" N ASN A 900 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 901 " --> pdb=" O ASP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.518A pdb=" N THR A 908 " --> pdb=" O ARG A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.677A pdb=" N SER A 953 " --> pdb=" O ASN A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 4.378A pdb=" N SER A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 4.504A pdb=" N ILE B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 167 through 194 removed outlier: 3.527A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 212 through 249 removed outlier: 3.761A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 277 Processing helix chain 'B' and resid 281 through 306 removed outlier: 4.696A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 321 through 330 removed outlier: 4.211A pdb=" N VAL B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.627A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.826A pdb=" N ASN B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 394 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 428 through 434 Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.692A pdb=" N MET B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 486 removed outlier: 3.842A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 478 " --> pdb=" O VAL B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 524 through 553 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 566 through 585 removed outlier: 3.631A pdb=" N THR B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 605 removed outlier: 3.618A pdb=" N ALA B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 removed outlier: 3.785A pdb=" N SER B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.749A pdb=" N VAL B 659 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 703 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.089A pdb=" N LEU B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 726 " --> pdb=" O GLN B 722 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 727 " --> pdb=" O ILE B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 750 through 767 removed outlier: 4.266A pdb=" N VAL B 754 " --> pdb=" O HIS B 750 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 821 through 824 Processing helix chain 'B' and resid 841 through 852 Proline residue: B 847 - end of helix Processing helix chain 'B' and resid 853 through 859 removed outlier: 3.997A pdb=" N LYS B 858 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 886 removed outlier: 4.325A pdb=" N ALA B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 900 removed outlier: 3.901A pdb=" N ILE B 899 " --> pdb=" O LEU B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 914 Processing helix chain 'B' and resid 924 through 935 Processing helix chain 'B' and resid 949 through 965 Processing helix chain 'B' and resid 986 through 998 Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 713 removed outlier: 4.337A pdb=" N GLY A 741 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 775 " --> pdb=" O VAL A1005 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.760A pdb=" N PHE B 708 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS B 645 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY B 675 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 647 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 646 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET B 774 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 973 " --> pdb=" O ILE B1006 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B1008 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 975 " --> pdb=" O ILE B1008 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2151 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: 4.50 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: 1.19 - 1.32: 2096 1.32 - 1.44: 3718 1.44 - 1.57: 7715 1.57 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 13653 Sorted by residual: bond pdb=" N SER B 422 " pdb=" CA SER B 422 " ideal model delta sigma weight residual 1.456 1.378 0.079 1.31e-02 5.83e+03 3.61e+01 bond pdb=" CD GLN B 165 " pdb=" OE1 GLN B 165 " ideal model delta sigma weight residual 1.231 1.329 -0.098 1.90e-02 2.77e+03 2.64e+01 bond pdb=" CD GLN A 563 " pdb=" OE1 GLN A 563 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.63e+01 bond pdb=" CG ASN B 359 " pdb=" OD1 ASN B 359 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" C ASN A 426 " pdb=" N PHE A 427 " ideal model delta sigma weight residual 1.334 1.272 0.062 1.24e-02 6.50e+03 2.51e+01 ... (remaining 13648 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.69: 313 105.69 - 112.83: 7247 112.83 - 119.96: 4741 119.96 - 127.10: 6078 127.10 - 134.23: 160 Bond angle restraints: 18539 Sorted by residual: angle pdb=" N LEU A 836 " pdb=" CA LEU A 836 " pdb=" C LEU A 836 " ideal model delta sigma weight residual 113.97 101.34 12.63 1.28e+00 6.10e-01 9.74e+01 angle pdb=" N ALA A 878 " pdb=" CA ALA A 878 " pdb=" C ALA A 878 " ideal model delta sigma weight residual 111.28 102.13 9.15 1.09e+00 8.42e-01 7.04e+01 angle pdb=" N ASP B 943 " pdb=" CA ASP B 943 " pdb=" C ASP B 943 " ideal model delta sigma weight residual 112.87 103.14 9.73 1.20e+00 6.94e-01 6.57e+01 angle pdb=" N LEU B 780 " pdb=" CA LEU B 780 " pdb=" C LEU B 780 " ideal model delta sigma weight residual 111.07 103.10 7.97 1.07e+00 8.73e-01 5.55e+01 angle pdb=" C LEU A1016 " pdb=" CA LEU A1016 " pdb=" CB LEU A1016 " ideal model delta sigma weight residual 111.89 101.99 9.90 1.42e+00 4.96e-01 4.86e+01 ... (remaining 18534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7140 17.59 - 35.18: 729 35.18 - 52.76: 140 52.76 - 70.35: 24 70.35 - 87.94: 6 Dihedral angle restraints: 8039 sinusoidal: 3138 harmonic: 4901 Sorted by residual: dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 151.41 -58.41 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CA GLY A 152 " pdb=" C GLY A 152 " pdb=" N VAL A 153 " pdb=" CA VAL A 153 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA GLY B 152 " pdb=" C GLY B 152 " pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta harmonic sigma weight residual -180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 8036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1948 0.085 - 0.169: 147 0.169 - 0.254: 17 0.254 - 0.338: 3 0.338 - 0.423: 3 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CA LYS A 784 " pdb=" N LYS A 784 " pdb=" C LYS A 784 " pdb=" CB LYS A 784 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA HIS A 750 " pdb=" N HIS A 750 " pdb=" C HIS A 750 " pdb=" CB HIS A 750 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA ARG B 334 " pdb=" N ARG B 334 " pdb=" C ARG B 334 " pdb=" CB ARG B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2115 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B1002 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B1003 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B1003 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1003 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 939 " -0.014 2.00e-02 2.50e+03 1.37e-02 4.66e+00 pdb=" CG TRP B 939 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 939 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 939 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 939 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 939 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 939 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 939 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 939 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 939 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 421 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.90e+00 pdb=" C CYS B 421 " 0.034 2.00e-02 2.50e+03 pdb=" O CYS B 421 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 422 " -0.012 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2661 2.76 - 3.29: 14136 3.29 - 3.83: 23694 3.83 - 4.36: 28426 4.36 - 4.90: 45802 Nonbonded interactions: 114719 Sorted by model distance: nonbonded pdb=" O SER A 345 " pdb=" OG SER A 533 " model vdw 2.222 2.440 nonbonded pdb=" O SER B 345 " pdb=" OG SER B 533 " model vdw 2.227 2.440 nonbonded pdb=" OE2 GLU B 755 " pdb=" OG SER B 987 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR A 156 " pdb=" OG SER A 296 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR B 156 " pdb=" OG SER B 296 " model vdw 2.234 2.440 ... (remaining 114714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 137 through 959 or (resid 960 and (name N or name CA or na \ me C or name O or name CB )) or resid 961 through 989 or (resid 990 and (name N \ or name CA or name C or name O or name CB )) or resid 991 through 1020)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 4.280 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 36.770 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 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 0.101 13653 Z= 0.340 Angle : 0.934 12.634 18539 Z= 0.609 Chirality : 0.051 0.423 2118 Planarity : 0.005 0.059 2320 Dihedral : 14.361 87.938 4887 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.19 % Allowed : 18.46 % Favored : 80.35 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1696 helix: 0.74 (0.17), residues: 930 sheet: -1.64 (0.56), residues: 71 loop : -2.75 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 939 HIS 0.003 0.001 HIS B 907 PHE 0.016 0.001 PHE B 665 TYR 0.023 0.001 TYR B 627 ARG 0.005 0.000 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 472 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 VAL cc_start: 0.7773 (t) cc_final: 0.7407 (t) REVERT: A 441 ILE cc_start: 0.6761 (tt) cc_final: 0.6041 (tt) REVERT: A 581 MET cc_start: 0.6009 (ttm) cc_final: 0.5533 (ttm) REVERT: A 599 LEU cc_start: 0.7811 (mt) cc_final: 0.7549 (mt) REVERT: A 671 LEU cc_start: 0.6431 (tp) cc_final: 0.6002 (tp) REVERT: A 776 MET cc_start: 0.3869 (pmm) cc_final: 0.3054 (pmm) REVERT: B 269 THR cc_start: 0.6876 (m) cc_final: 0.6360 (p) REVERT: B 505 PRO cc_start: 0.4614 (Cg_endo) cc_final: 0.3654 (Cg_exo) REVERT: B 642 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6921 (mmm-85) outliers start: 17 outliers final: 5 residues processed: 486 average time/residue: 0.2422 time to fit residues: 170.7433 Evaluate side-chains 287 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 81 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 566 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A 891 HIS A 999 GLN A1014 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 534 ASN B 566 ASN B 762 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13653 Z= 0.263 Angle : 0.816 12.785 18539 Z= 0.411 Chirality : 0.049 0.283 2118 Planarity : 0.006 0.125 2320 Dihedral : 5.354 47.633 1854 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.80 % Allowed : 22.17 % Favored : 72.03 % 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: -0.99 (0.20), residues: 1696 helix: 0.55 (0.17), residues: 948 sheet: -1.45 (0.56), residues: 80 loop : -2.38 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 172 HIS 0.013 0.001 HIS A 234 PHE 0.029 0.002 PHE A 341 TYR 0.042 0.002 TYR A 627 ARG 0.013 0.001 ARG A 642 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 304 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1018 PHE cc_start: 0.4844 (OUTLIER) cc_final: 0.3395 (t80) REVERT: B 642 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7195 (mmm-85) REVERT: B 658 LEU cc_start: 0.8088 (mp) cc_final: 0.7883 (mp) REVERT: B 870 ASN cc_start: 0.5637 (OUTLIER) cc_final: 0.4590 (p0) outliers start: 83 outliers final: 39 residues processed: 364 average time/residue: 0.2321 time to fit residues: 128.5306 Evaluate side-chains 310 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 268 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 645 CYS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 ASN Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN B 165 GLN B 534 ASN B 787 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 13653 Z= 0.453 Angle : 0.881 10.480 18539 Z= 0.466 Chirality : 0.051 0.288 2118 Planarity : 0.006 0.094 2320 Dihedral : 5.533 35.012 1846 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 39.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.16 % Rotamer: Outliers : 7.48 % Allowed : 25.45 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1696 helix: -0.01 (0.16), residues: 959 sheet: -2.08 (0.46), residues: 100 loop : -2.34 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 699 HIS 0.008 0.002 HIS A 234 PHE 0.039 0.004 PHE A 462 TYR 0.034 0.003 TYR B 156 ARG 0.011 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 257 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6524 (pp) REVERT: A 686 MET cc_start: 0.5577 (ttp) cc_final: 0.4695 (ttp) REVERT: A 725 MET cc_start: 0.7966 (ptt) cc_final: 0.7633 (ptt) REVERT: A 858 LYS cc_start: 0.4202 (OUTLIER) cc_final: 0.2881 (ptpp) REVERT: A 1018 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.4122 (t80) REVERT: B 642 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7233 (mmm-85) REVERT: B 685 ARG cc_start: 0.7177 (mpt180) cc_final: 0.6905 (mpt180) outliers start: 107 outliers final: 67 residues processed: 324 average time/residue: 0.2145 time to fit residues: 105.3445 Evaluate side-chains 294 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 223 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 533 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 642 ARG Chi-restraints excluded: chain B residue 645 CYS Chi-restraints excluded: chain B residue 661 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 359 ASN B 701 ASN B 787 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13653 Z= 0.306 Angle : 0.781 9.877 18539 Z= 0.396 Chirality : 0.047 0.259 2118 Planarity : 0.005 0.091 2320 Dihedral : 5.412 35.070 1845 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 6.92 % Allowed : 27.20 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1696 helix: 0.18 (0.16), residues: 957 sheet: -1.92 (0.47), residues: 100 loop : -2.23 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 699 HIS 0.008 0.001 HIS A 234 PHE 0.038 0.003 PHE A 462 TYR 0.030 0.002 TYR B 156 ARG 0.008 0.001 ARG B 718 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 254 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 THR cc_start: 0.7849 (p) cc_final: 0.7547 (p) REVERT: A 725 MET cc_start: 0.7809 (ptt) cc_final: 0.7432 (ptt) REVERT: A 858 LYS cc_start: 0.4712 (OUTLIER) cc_final: 0.3174 (ptpp) REVERT: A 872 MET cc_start: 0.3808 (tpt) cc_final: 0.1857 (mmm) REVERT: B 685 ARG cc_start: 0.7282 (mpt180) cc_final: 0.6935 (mpt180) REVERT: B 725 MET cc_start: 0.8266 (ppp) cc_final: 0.7866 (ppp) outliers start: 99 outliers final: 61 residues processed: 325 average time/residue: 0.2209 time to fit residues: 109.9187 Evaluate side-chains 294 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 232 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 834 TYR Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 147 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13653 Z= 0.321 Angle : 0.799 12.266 18539 Z= 0.403 Chirality : 0.048 0.289 2118 Planarity : 0.005 0.079 2320 Dihedral : 5.382 40.648 1841 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 7.55 % Allowed : 26.78 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1696 helix: 0.11 (0.16), residues: 957 sheet: -1.94 (0.47), residues: 100 loop : -2.14 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 138 HIS 0.006 0.001 HIS A 234 PHE 0.047 0.003 PHE A 462 TYR 0.027 0.002 TYR B 156 ARG 0.006 0.001 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 237 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.6002 (mmm) cc_final: 0.5237 (mmt) REVERT: A 447 MET cc_start: 0.7226 (ppp) cc_final: 0.6724 (ppp) REVERT: A 719 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7925 (mmt180) REVERT: A 725 MET cc_start: 0.7988 (ptt) cc_final: 0.7714 (ptt) REVERT: A 858 LYS cc_start: 0.5106 (OUTLIER) cc_final: 0.3663 (ptpp) REVERT: A 872 MET cc_start: 0.3745 (tpt) cc_final: 0.2332 (mmm) REVERT: A 1018 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.4771 (t80) REVERT: B 143 MET cc_start: 0.5201 (ttt) cc_final: 0.4791 (ttm) outliers start: 108 outliers final: 79 residues processed: 312 average time/residue: 0.2094 time to fit residues: 99.7427 Evaluate side-chains 305 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 223 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13653 Z= 0.244 Angle : 0.798 12.263 18539 Z= 0.385 Chirality : 0.049 0.365 2118 Planarity : 0.005 0.075 2320 Dihedral : 5.285 44.115 1841 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 29.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 6.08 % Allowed : 28.95 % Favored : 64.97 % 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: -1.02 (0.20), residues: 1696 helix: 0.34 (0.16), residues: 951 sheet: -1.70 (0.49), residues: 100 loop : -2.02 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 699 HIS 0.006 0.001 HIS B 637 PHE 0.039 0.002 PHE A 325 TYR 0.043 0.002 TYR A 386 ARG 0.006 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 248 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.5783 (mmm) cc_final: 0.5127 (mmt) REVERT: A 725 MET cc_start: 0.7813 (ptt) cc_final: 0.7549 (ptt) REVERT: A 785 MET cc_start: 0.3805 (mpp) cc_final: 0.3556 (mpp) REVERT: A 858 LYS cc_start: 0.5021 (OUTLIER) cc_final: 0.3694 (ptpp) REVERT: A 872 MET cc_start: 0.3648 (tpt) cc_final: 0.2307 (mmm) REVERT: A 1018 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.4751 (t80) REVERT: B 143 MET cc_start: 0.5123 (ttt) cc_final: 0.4518 (ttm) REVERT: B 346 ILE cc_start: 0.7458 (mm) cc_final: 0.7157 (mm) outliers start: 87 outliers final: 66 residues processed: 309 average time/residue: 0.2075 time to fit residues: 98.6236 Evaluate side-chains 299 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 231 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13653 Z= 0.258 Angle : 0.822 13.767 18539 Z= 0.399 Chirality : 0.049 0.374 2118 Planarity : 0.005 0.075 2320 Dihedral : 5.325 52.302 1841 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 30.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 6.01 % Allowed : 30.14 % Favored : 63.85 % 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: -0.98 (0.20), residues: 1696 helix: 0.34 (0.17), residues: 960 sheet: -1.69 (0.48), residues: 100 loop : -1.98 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 699 HIS 0.007 0.001 HIS B 637 PHE 0.055 0.002 PHE A 462 TYR 0.022 0.002 TYR B 513 ARG 0.017 0.001 ARG A 719 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 247 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.5792 (mmm) cc_final: 0.5144 (mmt) REVERT: A 725 MET cc_start: 0.7882 (ptt) cc_final: 0.7651 (ptt) REVERT: A 785 MET cc_start: 0.3774 (mpp) cc_final: 0.3532 (mpp) REVERT: A 858 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.3645 (ptpp) REVERT: A 872 MET cc_start: 0.3562 (tpt) cc_final: 0.1784 (mmm) REVERT: A 1018 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.4797 (t80) REVERT: B 143 MET cc_start: 0.5139 (ttt) cc_final: 0.4673 (ttm) REVERT: B 244 ASP cc_start: 0.5896 (m-30) cc_final: 0.5589 (m-30) REVERT: B 872 MET cc_start: -0.2297 (tpp) cc_final: -0.2566 (tpp) REVERT: B 874 GLN cc_start: 0.5596 (OUTLIER) cc_final: 0.4899 (pm20) outliers start: 86 outliers final: 70 residues processed: 311 average time/residue: 0.2010 time to fit residues: 97.1022 Evaluate side-chains 299 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 226 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 874 GLN Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 149 optimal weight: 0.0670 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13653 Z= 0.240 Angle : 0.850 14.354 18539 Z= 0.407 Chirality : 0.050 0.455 2118 Planarity : 0.005 0.063 2320 Dihedral : 5.330 57.689 1841 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 5.59 % Allowed : 30.77 % Favored : 63.64 % 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: -0.88 (0.20), residues: 1696 helix: 0.41 (0.17), residues: 963 sheet: -1.51 (0.47), residues: 98 loop : -1.96 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 172 HIS 0.007 0.001 HIS B 637 PHE 0.035 0.002 PHE A 341 TYR 0.023 0.002 TYR B 513 ARG 0.013 0.001 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 244 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.6023 (mmm) cc_final: 0.5815 (mmt) REVERT: A 447 MET cc_start: 0.7620 (ppp) cc_final: 0.6977 (ppp) REVERT: A 725 MET cc_start: 0.7783 (ptt) cc_final: 0.7489 (ptt) REVERT: A 785 MET cc_start: 0.3959 (mpp) cc_final: 0.3723 (mpp) REVERT: A 858 LYS cc_start: 0.5211 (OUTLIER) cc_final: 0.3748 (ptpp) REVERT: A 872 MET cc_start: 0.3707 (tpt) cc_final: 0.1988 (mmm) REVERT: A 1018 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.5020 (t80) REVERT: B 143 MET cc_start: 0.5271 (ttt) cc_final: 0.4904 (ttm) REVERT: B 872 MET cc_start: -0.2331 (tpp) cc_final: -0.2609 (tpp) REVERT: B 874 GLN cc_start: 0.5420 (OUTLIER) cc_final: 0.4671 (pm20) outliers start: 80 outliers final: 67 residues processed: 299 average time/residue: 0.2035 time to fit residues: 93.5353 Evaluate side-chains 302 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 874 GLN Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1001 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13653 Z= 0.252 Angle : 0.842 14.015 18539 Z= 0.408 Chirality : 0.050 0.397 2118 Planarity : 0.005 0.065 2320 Dihedral : 5.310 55.049 1841 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 31.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 5.24 % Allowed : 31.40 % Favored : 63.36 % 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: -0.92 (0.20), residues: 1696 helix: 0.36 (0.17), residues: 962 sheet: -1.33 (0.49), residues: 92 loop : -1.95 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 856 HIS 0.009 0.001 HIS B 549 PHE 0.045 0.002 PHE A 325 TYR 0.019 0.002 TYR B 513 ARG 0.006 0.001 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 241 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.7613 (ppp) cc_final: 0.7153 (ppp) REVERT: A 725 MET cc_start: 0.7780 (ptt) cc_final: 0.7551 (ptt) REVERT: A 785 MET cc_start: 0.3962 (mpp) cc_final: 0.3747 (mpp) REVERT: A 858 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4020 (ptpp) REVERT: A 872 MET cc_start: 0.3624 (tpt) cc_final: 0.3416 (mmt) REVERT: A 1018 PHE cc_start: 0.6012 (OUTLIER) cc_final: 0.5037 (t80) REVERT: B 143 MET cc_start: 0.5216 (ttt) cc_final: 0.4863 (ttm) REVERT: B 346 ILE cc_start: 0.7465 (mm) cc_final: 0.7097 (mm) outliers start: 75 outliers final: 65 residues processed: 291 average time/residue: 0.2085 time to fit residues: 93.9745 Evaluate side-chains 294 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 227 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ILE Chi-restraints excluded: chain B residue 1000 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13653 Z= 0.236 Angle : 0.867 17.088 18539 Z= 0.412 Chirality : 0.050 0.398 2118 Planarity : 0.005 0.056 2320 Dihedral : 5.257 51.727 1841 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 4.90 % Allowed : 32.45 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.21), residues: 1696 helix: 0.47 (0.17), residues: 961 sheet: -1.19 (0.49), residues: 92 loop : -1.88 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 172 HIS 0.007 0.001 HIS B 637 PHE 0.042 0.002 PHE A 325 TYR 0.039 0.002 TYR A 540 ARG 0.007 0.001 ARG A 887 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 245 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 MET cc_start: 0.7555 (ppp) cc_final: 0.7075 (ppp) REVERT: A 725 MET cc_start: 0.7650 (ptt) cc_final: 0.7378 (ptt) REVERT: A 858 LYS cc_start: 0.5382 (OUTLIER) cc_final: 0.4146 (ptpp) REVERT: A 872 MET cc_start: 0.3698 (tpt) cc_final: 0.2053 (mmm) REVERT: A 933 MET cc_start: 0.8322 (ptp) cc_final: 0.7785 (ppp) REVERT: A 1018 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5234 (t80) REVERT: B 143 MET cc_start: 0.4994 (ttt) cc_final: 0.4628 (ttm) REVERT: B 346 ILE cc_start: 0.7450 (mm) cc_final: 0.7149 (mm) REVERT: B 725 MET cc_start: 0.8037 (ppp) cc_final: 0.7454 (ppp) outliers start: 70 outliers final: 62 residues processed: 290 average time/residue: 0.2087 time to fit residues: 94.3173 Evaluate side-chains 296 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 232 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 642 ARG Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 858 LYS Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 990 TYR Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1018 PHE Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 457 ILE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 674 CYS Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 708 PHE Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 765 PHE Chi-restraints excluded: chain B residue 772 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 979 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.073949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.058158 restraints weight = 79344.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.059247 restraints weight = 61786.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.060087 restraints weight = 51355.670| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.7624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13653 Z= 0.259 Angle : 0.864 17.099 18539 Z= 0.415 Chirality : 0.050 0.394 2118 Planarity : 0.005 0.057 2320 Dihedral : 5.246 47.371 1841 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 31.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 4.62 % Allowed : 33.01 % Favored : 62.38 % 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: -0.83 (0.20), residues: 1696 helix: 0.40 (0.17), residues: 962 sheet: -1.24 (0.49), residues: 93 loop : -1.88 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 172 HIS 0.007 0.001 HIS B 637 PHE 0.042 0.002 PHE A 325 TYR 0.043 0.002 TYR A 540 ARG 0.015 0.001 ARG A 855 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.55 seconds wall clock time: 52 minutes 56.55 seconds (3176.55 seconds total)