Starting phenix.real_space_refine (version: dev) on Mon Feb 20 22:58:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/02_2023/7yg0_33803_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/02_2023/7yg0_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_33803/02_2023/7yg0_33803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/02_2023/7yg0_33803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/02_2023/7yg0_33803_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yg0_33803/02_2023/7yg0_33803_neut.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 7.21, per 1000 atoms: 0.54 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: 5.34 Conformation dependent library (CDL) restraints added in 1.9 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: 0.67 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: 3.87 Time building geometry restraints manager: 5.74 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 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. 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: 0.720 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: 4.490 Check model and map are aligned: 0.220 Process input model: 34.590 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 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 % 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 *********************** 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 : 1.514 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 outliers start: 17 outliers final: 5 residues processed: 486 average time/residue: 0.2376 time to fit residues: 167.9714 Evaluate side-chains 285 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 280 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2088 time to fit residues: 3.7247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.5763 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 13653 Z= 0.266 Angle : 0.827 14.372 18539 Z= 0.414 Chirality : 0.050 0.288 2118 Planarity : 0.006 0.126 2320 Dihedral : 5.001 19.556 1839 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 27.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1696 helix: 0.49 (0.17), residues: 948 sheet: -1.42 (0.57), residues: 80 loop : -2.37 (0.22), residues: 668 *********************** 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 386 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 308 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 38 residues processed: 362 average time/residue: 0.2218 time to fit residues: 122.0981 Evaluate side-chains 300 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1693 time to fit residues: 12.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 0.1980 chunk 167 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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 ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 13653 Z= 0.278 Angle : 0.771 11.167 18539 Z= 0.387 Chirality : 0.048 0.195 2118 Planarity : 0.005 0.045 2320 Dihedral : 4.941 23.425 1839 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer Outliers : 3.01 % 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: -0.96 (0.20), residues: 1696 helix: 0.49 (0.17), residues: 956 sheet: -1.97 (0.48), residues: 101 loop : -2.16 (0.23), residues: 639 *********************** 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 324 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 281 time to evaluate : 1.483 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 outliers start: 43 outliers final: 21 residues processed: 303 average time/residue: 0.2116 time to fit residues: 99.3580 Evaluate side-chains 265 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1269 time to fit residues: 6.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 80 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 13653 Z= 0.265 Angle : 0.756 11.788 18539 Z= 0.375 Chirality : 0.048 0.319 2118 Planarity : 0.004 0.044 2320 Dihedral : 4.886 21.777 1839 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.58 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1696 helix: 0.50 (0.17), residues: 957 sheet: -1.93 (0.48), residues: 95 loop : -2.09 (0.23), residues: 644 *********************** 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 310 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 260 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 294 average time/residue: 0.2130 time to fit residues: 98.0125 Evaluate side-chains 272 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1300 time to fit residues: 8.4084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 426 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS B 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 13653 Z= 0.225 Angle : 0.778 12.362 18539 Z= 0.376 Chirality : 0.048 0.369 2118 Planarity : 0.004 0.036 2320 Dihedral : 4.868 21.182 1839 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer Outliers : 2.59 % 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: -0.72 (0.20), residues: 1696 helix: 0.62 (0.17), residues: 956 sheet: -1.45 (0.53), residues: 80 loop : -2.00 (0.24), residues: 660 *********************** 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 304 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 267 time to evaluate : 1.656 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 outliers start: 37 outliers final: 14 residues processed: 291 average time/residue: 0.2176 time to fit residues: 97.6880 Evaluate side-chains 249 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1239 time to fit residues: 5.2936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.0970 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 566 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS B 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 13653 Z= 0.227 Angle : 0.765 12.885 18539 Z= 0.374 Chirality : 0.048 0.392 2118 Planarity : 0.004 0.042 2320 Dihedral : 4.833 21.812 1839 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer Outliers : 3.08 % 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: -0.74 (0.20), residues: 1696 helix: 0.59 (0.17), residues: 956 sheet: -1.58 (0.50), residues: 95 loop : -1.95 (0.24), residues: 645 *********************** 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 295 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 251 time to evaluate : 1.675 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 outliers start: 44 outliers final: 23 residues processed: 276 average time/residue: 0.2326 time to fit residues: 97.8701 Evaluate side-chains 264 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1449 time to fit residues: 8.1821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 138 optimal weight: 0.0040 chunk 91 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 101 optimal weight: 6.9990 overall best weight: 2.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 668 ASN B 234 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 13653 Z= 0.258 Angle : 0.801 13.013 18539 Z= 0.388 Chirality : 0.048 0.392 2118 Planarity : 0.005 0.051 2320 Dihedral : 4.850 21.868 1839 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.58 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1696 helix: 0.56 (0.17), residues: 952 sheet: -1.60 (0.51), residues: 96 loop : -1.92 (0.24), residues: 648 *********************** 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 271 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 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 outliers start: 27 outliers final: 14 residues processed: 260 average time/residue: 0.2034 time to fit residues: 82.6531 Evaluate side-chains 249 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1245 time to fit residues: 5.1554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 891 HIS B 234 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 13653 Z= 0.241 Angle : 0.841 14.736 18539 Z= 0.393 Chirality : 0.049 0.374 2118 Planarity : 0.005 0.051 2320 Dihedral : 4.828 21.737 1839 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Rotamer Outliers : 0.91 % 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: -0.69 (0.20), residues: 1696 helix: 0.60 (0.17), residues: 953 sheet: -1.47 (0.50), residues: 96 loop : -1.89 (0.24), residues: 647 *********************** 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 268 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 255 time to evaluate : 1.532 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 outliers start: 13 outliers final: 5 residues processed: 264 average time/residue: 0.2200 time to fit residues: 89.8015 Evaluate side-chains 236 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 1.482 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1238 time to fit residues: 3.3281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 9.9990 chunk 143 optimal weight: 0.0670 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 161 optimal weight: 0.4980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 HIS B 286 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.6554 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= 0.239 Angle : 0.861 14.148 18539 Z= 0.405 Chirality : 0.050 0.373 2118 Planarity : 0.005 0.074 2320 Dihedral : 4.838 20.254 1839 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.58 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1696 helix: 0.59 (0.17), residues: 956 sheet: -1.32 (0.50), residues: 96 loop : -1.84 (0.24), residues: 644 *********************** 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 259 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 1.601 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 outliers start: 15 outliers final: 7 residues processed: 252 average time/residue: 0.2146 time to fit residues: 84.3835 Evaluate side-chains 235 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1417 time to fit residues: 3.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.0770 chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 0.1980 chunk 82 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 891 HIS B 234 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 13653 Z= 0.281 Angle : 0.877 14.555 18539 Z= 0.421 Chirality : 0.050 0.304 2118 Planarity : 0.005 0.084 2320 Dihedral : 4.918 19.204 1839 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer Outliers : 0.63 % 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: -0.73 (0.20), residues: 1696 helix: 0.50 (0.17), residues: 958 sheet: -1.30 (0.50), residues: 95 loop : -1.85 (0.24), residues: 643 ********************** 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 248 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 1.564 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 outliers start: 9 outliers final: 5 residues processed: 246 average time/residue: 0.2310 time to fit residues: 87.3697 Evaluate side-chains 239 residues out of total 1436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2024 time to fit residues: 3.6912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 135 optimal weight: 0.2980 chunk 56 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 HIS B 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.079660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.063806 restraints weight = 74938.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.064911 restraints weight = 60369.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.065775 restraints weight = 50914.654| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 13653 Z= 0.256 Angle : 0.889 13.920 18539 Z= 0.421 Chirality : 0.052 0.427 2118 Planarity : 0.004 0.045 2320 Dihedral : 4.928 20.010 1839 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.48 % Favored : 94.46 % Rotamer Outliers : 0.49 % 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: -0.73 (0.20), residues: 1696 helix: 0.51 (0.17), residues: 953 sheet: -1.26 (0.51), residues: 94 loop : -1.86 (0.24), residues: 649 =============================================================================== Job complete usr+sys time: 2670.74 seconds wall clock time: 49 minutes 33.34 seconds (2973.34 seconds total)