Starting phenix.real_space_refine on Thu Feb 15 01:10:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e20_30948/02_2024/7e20_30948_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e20_30948/02_2024/7e20_30948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e20_30948/02_2024/7e20_30948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e20_30948/02_2024/7e20_30948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e20_30948/02_2024/7e20_30948_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e20_30948/02_2024/7e20_30948_neut.pdb" } resolution = 2.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 6906 2.51 5 N 1741 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 786": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10694 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7712 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 43, 'TRANS': 950} Chain: "B" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2404 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 273} Chain: "C" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Unusual residues: {' K': 3, ' MG': 1, 'PC1': 1, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'NAG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.04, per 1000 atoms: 0.56 Number of scatterers: 10694 At special positions: 0 Unit cell: (100.004, 94.569, 185.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 58 16.00 P 1 15.00 Mg 1 11.99 O 1984 8.00 N 1741 7.00 C 6906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 249 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 584 " distance=2.01 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.18 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 403 " - " ASN B 265 " " NAG D 1 " - " ASN B 158 " Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 3.3 seconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 48.3% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.665A pdb=" N ARG A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.972A pdb=" N GLU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 95 through 98 removed outlier: 3.868A pdb=" N GLY A 98 " --> pdb=" O GLN A 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 99 through 120 removed outlier: 4.227A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 removed outlier: 3.780A pdb=" N TYR A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.990A pdb=" N SER A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.886A pdb=" N VAL A 185 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 306 removed outlier: 3.739A pdb=" N HIS A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 316 through 330 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.656A pdb=" N ARG A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 4.040A pdb=" N THR A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 367' Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.742A pdb=" N LEU A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.554A pdb=" N LYS A 444 " --> pdb=" O PRO A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 4.115A pdb=" N LEU A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.570A pdb=" N LYS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.680A pdb=" N GLY A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.875A pdb=" N VAL A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.694A pdb=" N LYS A 671 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 667 through 672' Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.624A pdb=" N ASP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 708 removed outlier: 4.077A pdb=" N LEU A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 755 through 782 removed outlier: 4.224A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A 773 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix removed outlier: 3.632A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 812 removed outlier: 3.612A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 811 " --> pdb=" O ILE A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 821 Processing helix chain 'A' and resid 822 through 825 Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.557A pdb=" N ARG A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 removed outlier: 3.633A pdb=" N GLN A 856 " --> pdb=" O MET A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.725A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 873 " --> pdb=" O TYR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 937 removed outlier: 3.763A pdb=" N ILE A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 931 " --> pdb=" O VAL A 927 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.581A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 removed outlier: 3.606A pdb=" N ALA A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 990 removed outlier: 3.584A pdb=" N TRP A 988 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 989 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 990 " --> pdb=" O TRP A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.648A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 59 removed outlier: 3.994A pdb=" N ILE B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.846A pdb=" N VAL B 72 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.559A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.556A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.892A pdb=" N GLY B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'C' and resid 22 through 46 removed outlier: 4.321A pdb=" N VAL C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.552A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 227 removed outlier: 4.144A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.450A pdb=" N GLY A 731 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 750 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 733 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 715 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 398 through 399 removed outlier: 6.791A pdb=" N SER A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 587 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.120A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 124 437 hydrogen bonds defined for protein. 1242 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: 3.97 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1774 1.31 - 1.44: 2749 1.44 - 1.57: 6260 1.57 - 1.70: 56 1.70 - 1.83: 86 Bond restraints: 10925 Sorted by residual: bond pdb=" CAI Y01 C1501 " pdb=" CAZ Y01 C1501 " ideal model delta sigma weight residual 1.332 1.555 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" CAI Y01 B 401 " pdb=" CAZ Y01 B 401 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAI Y01 A1105 " pdb=" CAZ Y01 A1105 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAI Y01 B 402 " pdb=" CAZ Y01 B 402 " ideal model delta sigma weight residual 1.332 1.552 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAI Y01 A1107 " pdb=" CAZ Y01 A1107 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 10920 not shown) Histogram of bond angle deviations from ideal: 83.14 - 93.47: 6 93.47 - 103.81: 170 103.81 - 114.15: 6486 114.15 - 124.48: 7957 124.48 - 134.82: 207 Bond angle restraints: 14826 Sorted by residual: angle pdb=" CAD Y01 B 401 " pdb=" CBH Y01 B 401 " pdb=" CBF Y01 B 401 " ideal model delta sigma weight residual 111.82 83.78 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" CAD Y01 B 402 " pdb=" CBH Y01 B 402 " pdb=" CBF Y01 B 402 " ideal model delta sigma weight residual 111.82 84.17 27.65 3.00e+00 1.11e-01 8.50e+01 angle pdb=" CAD Y01 B 401 " pdb=" CBH Y01 B 401 " pdb=" CAT Y01 B 401 " ideal model delta sigma weight residual 109.59 83.48 26.11 3.00e+00 1.11e-01 7.58e+01 angle pdb=" CAD Y01 B 402 " pdb=" CBH Y01 B 402 " pdb=" CAT Y01 B 402 " ideal model delta sigma weight residual 109.59 83.54 26.05 3.00e+00 1.11e-01 7.54e+01 angle pdb=" CAD Y01 B 402 " pdb=" CBH Y01 B 402 " pdb=" CAZ Y01 B 402 " ideal model delta sigma weight residual 108.53 83.14 25.39 3.00e+00 1.11e-01 7.16e+01 ... (remaining 14821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6550 35.66 - 71.33: 217 71.33 - 106.99: 54 106.99 - 142.65: 98 142.65 - 178.31: 13 Dihedral angle restraints: 6932 sinusoidal: 3126 harmonic: 3806 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS A 249 " pdb=" CB CYS A 249 " ideal model delta sinusoidal sigma weight residual -86.00 -166.31 80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA ALA A 152 " pdb=" C ALA A 152 " pdb=" N LYS A 153 " pdb=" CA LYS A 153 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR B 242 " pdb=" C TYR B 242 " pdb=" N TYR B 243 " pdb=" CA TYR B 243 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.200: 1651 1.200 - 2.400: 0 2.400 - 3.601: 0 3.601 - 4.801: 2 4.801 - 6.001: 28 Chirality restraints: 1681 Sorted by residual: chirality pdb=" CBI Y01 A1105 " pdb=" CAU Y01 A1105 " pdb=" CBE Y01 A1105 " pdb=" CBG Y01 A1105 " both_signs ideal model delta sigma weight residual False 2.94 -3.06 6.00 2.00e-01 2.50e+01 9.00e+02 chirality pdb=" CBI Y01 C1501 " pdb=" CAU Y01 C1501 " pdb=" CBE Y01 C1501 " pdb=" CBG Y01 C1501 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.99 2.00e-01 2.50e+01 8.97e+02 chirality pdb=" CBI Y01 B 402 " pdb=" CAU Y01 B 402 " pdb=" CBE Y01 B 402 " pdb=" CBG Y01 B 402 " both_signs ideal model delta sigma weight residual False 2.94 -3.04 5.98 2.00e-01 2.50e+01 8.94e+02 ... (remaining 1678 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 199 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO B 200 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 788 " -0.047 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 789 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 789 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 789 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 132 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO B 133 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.034 5.00e-02 4.00e+02 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 654 2.73 - 3.33: 11381 3.33 - 3.93: 19777 3.93 - 4.54: 27329 4.54 - 5.14: 42493 Nonbonded interactions: 101634 Sorted by model distance: nonbonded pdb=" O THR A 378 " pdb="MG MG A1104 " model vdw 2.127 2.170 nonbonded pdb=" CAP Y01 A1107 " pdb=" CAC Y01 B 402 " model vdw 2.204 3.860 nonbonded pdb=" OD1 ASP A 717 " pdb="MG MG A1104 " model vdw 2.208 2.170 nonbonded pdb=" CD1 ILE A 881 " pdb=" OAG Y01 A1107 " model vdw 2.218 3.460 nonbonded pdb=" SD MET A 859 " pdb=" CAA Y01 A1107 " model vdw 2.272 3.820 ... (remaining 101629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 2.320 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 34.190 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.012 0.223 10925 Z= 0.779 Angle : 1.328 28.039 14826 Z= 0.623 Chirality : 0.716 6.001 1681 Planarity : 0.008 0.077 1869 Dihedral : 27.528 178.312 4473 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.77 % Favored : 92.70 % Rotamer: Outliers : 1.15 % Allowed : 6.61 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -3.51 (0.19), residues: 1315 helix: -2.52 (0.16), residues: 559 sheet: -0.95 (0.36), residues: 162 loop : -2.45 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 392 HIS 0.005 0.002 HIS A 44 PHE 0.040 0.003 PHE A 291 TYR 0.040 0.002 TYR B 243 ARG 0.012 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8164 (mt) cc_final: 0.7882 (tm) REVERT: A 211 CYS cc_start: 0.5266 (OUTLIER) cc_final: 0.4867 (p) REVERT: A 423 ARG cc_start: 0.7828 (ttp-110) cc_final: 0.7627 (ptp90) REVERT: A 507 MET cc_start: 0.7515 (ptt) cc_final: 0.7120 (pp-130) REVERT: A 593 ASP cc_start: 0.8101 (t0) cc_final: 0.7889 (t70) REVERT: A 654 GLN cc_start: 0.7626 (mt0) cc_final: 0.7284 (mt0) REVERT: A 847 GLU cc_start: 0.7507 (pm20) cc_final: 0.7207 (pm20) REVERT: B 17 TRP cc_start: 0.6202 (t-100) cc_final: 0.5909 (t60) outliers start: 13 outliers final: 1 residues processed: 166 average time/residue: 1.5467 time to fit residues: 273.1296 Evaluate side-chains 104 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 0.0270 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 225 GLN A 390 HIS A 398 HIS A 436 ASN A 437 GLN A 486 ASN A 524 HIS A 539 GLN A 540 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 656 ASN A 797 ASN A 882 HIS A 905 GLN B 55 GLN B 104 ASN B 141 HIS B 163 ASN B 282 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10925 Z= 0.195 Angle : 1.487 32.493 14826 Z= 0.552 Chirality : 0.146 1.881 1681 Planarity : 0.006 0.057 1869 Dihedral : 29.493 178.988 1964 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.94 % Allowed : 12.33 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.82 (0.22), residues: 1315 helix: -0.66 (0.21), residues: 559 sheet: -0.54 (0.39), residues: 155 loop : -1.88 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 392 HIS 0.002 0.001 HIS A 290 PHE 0.020 0.002 PHE A 291 TYR 0.030 0.001 TYR B 243 ARG 0.007 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.279 Fit side-chains REVERT: A 170 LEU cc_start: 0.8101 (mt) cc_final: 0.7832 (tm) REVERT: A 269 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7890 (mtp180) REVERT: A 654 GLN cc_start: 0.7621 (mt0) cc_final: 0.7271 (mt0) REVERT: B 17 TRP cc_start: 0.6234 (t-100) cc_final: 0.5909 (t60) REVERT: C 27 ARG cc_start: 0.8095 (ttm170) cc_final: 0.7840 (ttm170) outliers start: 22 outliers final: 6 residues processed: 134 average time/residue: 1.3339 time to fit residues: 192.1858 Evaluate side-chains 104 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 142 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10925 Z= 0.209 Angle : 1.477 32.042 14826 Z= 0.546 Chirality : 0.144 1.866 1681 Planarity : 0.005 0.049 1869 Dihedral : 29.344 179.851 1961 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.03 % Allowed : 14.54 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.10 (0.23), residues: 1315 helix: 0.12 (0.22), residues: 560 sheet: -0.43 (0.39), residues: 155 loop : -1.62 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 392 HIS 0.003 0.001 HIS A 290 PHE 0.016 0.001 PHE A 291 TYR 0.024 0.001 TYR B 243 ARG 0.009 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.253 Fit side-chains REVERT: A 170 LEU cc_start: 0.8034 (mt) cc_final: 0.7754 (tm) REVERT: A 192 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6930 (tt0) REVERT: A 269 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7897 (mtp180) REVERT: A 654 GLN cc_start: 0.7647 (mt0) cc_final: 0.7330 (mt0) REVERT: A 847 GLU cc_start: 0.7375 (pm20) cc_final: 0.7105 (pm20) REVERT: B 17 TRP cc_start: 0.6255 (t-100) cc_final: 0.5924 (t60) REVERT: B 141 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.5668 (t-170) outliers start: 23 outliers final: 8 residues processed: 121 average time/residue: 1.1715 time to fit residues: 154.1487 Evaluate side-chains 101 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 0.0000 chunk 56 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 GLN A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10925 Z= 0.333 Angle : 1.503 31.969 14826 Z= 0.563 Chirality : 0.144 1.852 1681 Planarity : 0.005 0.051 1869 Dihedral : 29.322 179.911 1961 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.17 % Allowed : 15.68 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.95 (0.23), residues: 1315 helix: 0.24 (0.22), residues: 565 sheet: -0.46 (0.38), residues: 165 loop : -1.52 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 418 HIS 0.003 0.001 HIS A 290 PHE 0.023 0.002 PHE A 922 TYR 0.032 0.002 TYR B 243 ARG 0.006 0.001 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 1.269 Fit side-chains REVERT: A 170 LEU cc_start: 0.8065 (mt) cc_final: 0.7750 (tm) REVERT: A 192 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6937 (tt0) REVERT: A 269 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7924 (mtp180) REVERT: A 391 MET cc_start: 0.8056 (mtm) cc_final: 0.7817 (mtt) REVERT: A 654 GLN cc_start: 0.7648 (mt0) cc_final: 0.7327 (mt0) REVERT: A 847 GLU cc_start: 0.7362 (pm20) cc_final: 0.7066 (pm20) REVERT: B 17 TRP cc_start: 0.6298 (t-100) cc_final: 0.5937 (t60) REVERT: B 177 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9038 (mp) outliers start: 36 outliers final: 15 residues processed: 120 average time/residue: 1.2068 time to fit residues: 156.9483 Evaluate side-chains 109 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 811 ASP Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 1 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.0040 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.5674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10925 Z= 0.195 Angle : 1.466 32.221 14826 Z= 0.539 Chirality : 0.144 1.858 1681 Planarity : 0.005 0.048 1869 Dihedral : 29.145 179.832 1961 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.38 % Allowed : 16.92 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.60 (0.23), residues: 1315 helix: 0.57 (0.23), residues: 568 sheet: -0.21 (0.40), residues: 155 loop : -1.40 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 418 HIS 0.002 0.001 HIS A 290 PHE 0.013 0.001 PHE A 291 TYR 0.024 0.001 TYR B 243 ARG 0.005 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.200 Fit side-chains REVERT: A 170 LEU cc_start: 0.8046 (mt) cc_final: 0.7760 (tm) REVERT: A 269 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7923 (mtp180) REVERT: A 391 MET cc_start: 0.8051 (mtm) cc_final: 0.7781 (mtt) REVERT: A 419 LEU cc_start: 0.7564 (mp) cc_final: 0.7362 (pp) REVERT: A 423 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6733 (ptp90) REVERT: A 530 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4734 (tm) REVERT: A 591 MET cc_start: 0.8368 (mtm) cc_final: 0.8124 (mtp) REVERT: A 654 GLN cc_start: 0.7622 (mt0) cc_final: 0.7289 (mt0) REVERT: A 847 GLU cc_start: 0.7379 (pm20) cc_final: 0.7073 (pm20) REVERT: A 954 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8723 (tp) REVERT: B 17 TRP cc_start: 0.6283 (t-100) cc_final: 0.5926 (t60) REVERT: B 141 HIS cc_start: 0.5803 (OUTLIER) cc_final: 0.5506 (t-170) outliers start: 27 outliers final: 10 residues processed: 127 average time/residue: 1.3509 time to fit residues: 185.5628 Evaluate side-chains 107 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 954 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 0.0010 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 540 ASN A 876 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10925 Z= 0.167 Angle : 1.448 32.255 14826 Z= 0.527 Chirality : 0.144 1.866 1681 Planarity : 0.004 0.046 1869 Dihedral : 28.991 179.206 1961 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.47 % Allowed : 17.27 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1315 helix: 0.93 (0.23), residues: 565 sheet: -0.10 (0.40), residues: 155 loop : -1.22 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 418 HIS 0.002 0.001 HIS A 503 PHE 0.011 0.001 PHE B 295 TYR 0.017 0.001 TYR B 243 ARG 0.005 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.268 Fit side-chains REVERT: A 391 MET cc_start: 0.8048 (mtm) cc_final: 0.7775 (mtt) REVERT: A 423 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6747 (ptp90) REVERT: A 479 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5841 (pp20) REVERT: A 654 GLN cc_start: 0.7615 (mt0) cc_final: 0.7262 (mt0) REVERT: B 17 TRP cc_start: 0.6334 (t-100) cc_final: 0.6000 (t60) outliers start: 28 outliers final: 10 residues processed: 130 average time/residue: 1.2495 time to fit residues: 175.9785 Evaluate side-chains 105 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10925 Z= 0.310 Angle : 1.492 31.909 14826 Z= 0.556 Chirality : 0.145 1.897 1681 Planarity : 0.005 0.050 1869 Dihedral : 29.090 179.469 1961 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.91 % Allowed : 17.62 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.41 (0.23), residues: 1315 helix: 0.65 (0.23), residues: 570 sheet: -0.18 (0.39), residues: 165 loop : -1.19 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 392 HIS 0.003 0.001 HIS A 620 PHE 0.021 0.002 PHE A 922 TYR 0.029 0.002 TYR B 243 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 1.240 Fit side-chains REVERT: A 170 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7094 (mm) REVERT: A 192 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: A 391 MET cc_start: 0.8158 (mtm) cc_final: 0.7874 (mtt) REVERT: A 423 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6737 (ptp90) REVERT: A 479 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5796 (pp20) REVERT: B 17 TRP cc_start: 0.6298 (t-100) cc_final: 0.5954 (t60) REVERT: B 177 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9029 (mp) outliers start: 33 outliers final: 19 residues processed: 120 average time/residue: 1.2146 time to fit residues: 157.7353 Evaluate side-chains 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 235 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 0.0470 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10925 Z= 0.191 Angle : 1.460 32.208 14826 Z= 0.535 Chirality : 0.144 1.857 1681 Planarity : 0.004 0.047 1869 Dihedral : 28.930 179.140 1961 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.38 % Allowed : 18.50 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.17 (0.24), residues: 1315 helix: 0.88 (0.23), residues: 570 sheet: -0.15 (0.39), residues: 165 loop : -1.08 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 392 HIS 0.002 0.001 HIS A 503 PHE 0.019 0.001 PHE B 139 TYR 0.020 0.001 TYR B 243 ARG 0.004 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 1.214 Fit side-chains REVERT: A 170 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7078 (mm) REVERT: A 192 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: A 391 MET cc_start: 0.8016 (mtm) cc_final: 0.7805 (mtt) REVERT: A 418 TRP cc_start: 0.7580 (t-100) cc_final: 0.7156 (t-100) REVERT: A 423 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6840 (ptp90) REVERT: A 847 GLU cc_start: 0.7466 (pm20) cc_final: 0.7209 (pm20) REVERT: B 17 TRP cc_start: 0.6281 (t-100) cc_final: 0.5946 (t60) REVERT: B 177 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8970 (mp) outliers start: 27 outliers final: 11 residues processed: 119 average time/residue: 1.2406 time to fit residues: 159.9292 Evaluate side-chains 106 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 235 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.0970 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 540 ASN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10925 Z= 0.173 Angle : 1.452 32.153 14826 Z= 0.530 Chirality : 0.145 1.868 1681 Planarity : 0.004 0.046 1869 Dihedral : 28.809 179.141 1961 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.67 % Allowed : 19.21 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.06 (0.24), residues: 1315 helix: 1.12 (0.23), residues: 568 sheet: -0.10 (0.39), residues: 165 loop : -0.98 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.002 0.000 HIS A 503 PHE 0.017 0.001 PHE B 139 TYR 0.018 0.001 TYR B 243 ARG 0.004 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.244 Fit side-chains REVERT: A 192 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: A 391 MET cc_start: 0.7971 (mtm) cc_final: 0.7766 (mtt) REVERT: A 418 TRP cc_start: 0.7515 (t-100) cc_final: 0.7133 (t-100) REVERT: B 17 TRP cc_start: 0.6335 (t-100) cc_final: 0.5994 (t60) REVERT: B 177 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8868 (mp) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 1.3225 time to fit residues: 161.6466 Evaluate side-chains 107 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.0470 chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 GLN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10925 Z= 0.156 Angle : 1.442 32.144 14826 Z= 0.524 Chirality : 0.145 1.870 1681 Planarity : 0.004 0.045 1869 Dihedral : 28.721 178.906 1961 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.41 % Allowed : 19.47 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.27 (0.24), residues: 1315 helix: 1.31 (0.23), residues: 567 sheet: 0.00 (0.40), residues: 158 loop : -0.87 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 392 HIS 0.003 0.001 HIS A 493 PHE 0.017 0.001 PHE B 139 TYR 0.013 0.001 TYR A 488 ARG 0.004 0.000 ARG A 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.282 Fit side-chains REVERT: A 391 MET cc_start: 0.7935 (mtm) cc_final: 0.7706 (mtt) REVERT: B 17 TRP cc_start: 0.6342 (t-100) cc_final: 0.6015 (t60) outliers start: 16 outliers final: 9 residues processed: 114 average time/residue: 1.2110 time to fit residues: 149.6658 Evaluate side-chains 102 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.144344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107019 restraints weight = 16461.411| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.76 r_work: 0.3270 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10925 Z= 0.265 Angle : 1.475 31.827 14826 Z= 0.546 Chirality : 0.145 1.904 1681 Planarity : 0.005 0.049 1869 Dihedral : 28.832 179.649 1961 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.50 % Allowed : 20.00 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.05 (0.24), residues: 1315 helix: 0.99 (0.23), residues: 570 sheet: 0.05 (0.39), residues: 165 loop : -0.90 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.003 0.001 HIS A 493 PHE 0.020 0.002 PHE B 139 TYR 0.023 0.002 TYR B 243 ARG 0.004 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.97 seconds wall clock time: 68 minutes 59.21 seconds (4139.21 seconds total)