Starting phenix.real_space_refine on Sun Feb 18 11:01:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eu7_31308/02_2024/7eu7_31308_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 93 5.16 5 Cl 1 4.86 5 C 14039 2.51 5 N 3729 2.21 5 O 3911 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "D GLU 904": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21773 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5530 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 33, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 682 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 559 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 17, 'TYR:plan': 1, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 37, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 445 Chain: "B" Number of atoms: 5272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5272 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 935 Unresolved non-hydrogen angles: 1172 Unresolved non-hydrogen dihedrals: 770 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 14, 'TRP:plan': 3, 'ASP:plan': 35, 'PHE:plan': 13, 'GLU:plan': 41, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 573 Chain: "C" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5387 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 33, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 826 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 675 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 20, 'TYR:plan': 1, 'ASN:plan1': 13, 'HIS:plan': 4, 'PHE:plan': 8, 'GLU:plan': 43, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 535 Chain: "D" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5206 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 997 Unresolved non-hydrogen angles: 1247 Unresolved non-hydrogen dihedrals: 807 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 21, 'TRP:plan': 2, 'ASP:plan': 39, 'PHE:plan': 12, 'GLU:plan': 42, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 593 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'NAG': 9} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 130 Unusual residues: {'NAG': 9} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'JC9': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.98, per 1000 atoms: 0.55 Number of scatterers: 21773 At special positions: 0 Unit cell: (110.39, 141.93, 181.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 93 16.00 O 3911 8.00 N 3729 7.00 C 14039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.05 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.04 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.02 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 800 " 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 NAG-ASN " NAG A 901 " - " ASN A 61 " " NAG A 902 " - " ASN A 203 " " NAG A 903 " - " ASN A 239 " " NAG A 904 " - " ASN A 276 " " NAG A 905 " - " ASN A 350 " " NAG A 906 " - " ASN A 368 " " NAG A 907 " - " ASN A 440 " " NAG A 908 " - " ASN A 471 " " NAG A 909 " - " ASN A 771 " " NAG B 901 " - " ASN B 340 " " NAG B 902 " - " ASN B 380 " " NAG B 903 " - " ASN B 687 " " NAG C 901 " - " ASN C 61 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 239 " " NAG C 904 " - " ASN C 276 " " NAG C 905 " - " ASN C 350 " " NAG C 906 " - " ASN C 368 " " NAG C 907 " - " ASN C 440 " " NAG C 908 " - " ASN C 471 " " NAG C 909 " - " ASN C 771 " " NAG D 901 " - " ASN D 340 " " NAG D 902 " - " ASN D 380 " " NAG D 903 " - " ASN D 687 " Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 4.7 seconds 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 30 sheets defined 38.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 36 through 52 Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 145 through 157 removed outlier: 4.350A pdb=" N VAL A 157 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.717A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.655A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 560 through 581 removed outlier: 3.892A pdb=" N GLY A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 Processing helix chain 'A' and resid 627 through 656 Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.886A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.878A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 4.007A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 Processing helix chain 'A' and resid 810 through 839 removed outlier: 4.262A pdb=" N ALA A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY A 815 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N MET A 818 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 827 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE A 828 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 829 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 838 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.837A pdb=" N GLU B 50 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG B 52 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 180 through 192 Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.994A pdb=" N LYS B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.677A pdb=" N VAL B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 288 through 309 removed outlier: 4.430A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 459 through 471 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 556 through 577 Processing helix chain 'B' and resid 600 through 613 Processing helix chain 'B' and resid 625 through 654 removed outlier: 3.725A pdb=" N ILE B 629 " --> pdb=" O THR B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 671 No H-bonds generated for 'chain 'B' and resid 668 through 671' Processing helix chain 'B' and resid 689 through 697 Processing helix chain 'B' and resid 699 through 708 removed outlier: 3.518A pdb=" N GLN B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 704 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B 708 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 732 through 741 Processing helix chain 'B' and resid 772 through 784 removed outlier: 4.127A pdb=" N LEU B 777 " --> pdb=" O ARG B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 818 through 840 Processing helix chain 'C' and resid 36 through 52 removed outlier: 3.553A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 126 through 129 Processing helix chain 'C' and resid 144 through 157 removed outlier: 4.083A pdb=" N VAL C 157 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.792A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.578A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 560 through 581 removed outlier: 3.863A pdb=" N VAL C 566 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 568 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 569 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 570 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 613 Processing helix chain 'C' and resid 627 through 657 Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 694 Processing helix chain 'C' and resid 700 through 708 removed outlier: 3.958A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.213A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 removed outlier: 4.399A pdb=" N VAL C 772 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N SER C 773 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE C 776 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 778 " --> pdb=" O SER C 775 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS C 780 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 Processing helix chain 'C' and resid 810 through 815 Processing helix chain 'C' and resid 817 through 840 removed outlier: 4.470A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG C 839 " --> pdb=" O ILE C 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.077A pdb=" N GLU D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 180 through 193 Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.813A pdb=" N LYS D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.658A pdb=" N VAL D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 459 through 471 Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 557 through 577 Processing helix chain 'D' and resid 600 through 613 Processing helix chain 'D' and resid 625 through 654 removed outlier: 3.880A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 671 No H-bonds generated for 'chain 'D' and resid 668 through 671' Processing helix chain 'D' and resid 689 through 697 Processing helix chain 'D' and resid 699 through 708 removed outlier: 4.549A pdb=" N LYS D 707 " --> pdb=" O GLN D 703 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 722 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 772 through 784 removed outlier: 4.158A pdb=" N LEU D 777 " --> pdb=" O ARG D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 814 through 840 removed outlier: 3.550A pdb=" N MET D 823 " --> pdb=" O GLY D 819 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.526A pdb=" N VAL A 246 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 248 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 249 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 269 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 266 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 365 through 367 Processing sheet with id= D, first strand: chain 'A' and resid 399 through 401 removed outlier: 6.047A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 409 through 412 Processing sheet with id= F, first strand: chain 'A' and resid 437 through 439 Processing sheet with id= G, first strand: chain 'A' and resid 487 through 489 Processing sheet with id= H, first strand: chain 'A' and resid 729 through 732 Processing sheet with id= I, first strand: chain 'B' and resid 68 through 73 removed outlier: 3.523A pdb=" N GLY B 126 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 173 through 175 removed outlier: 6.300A pdb=" N ILE B 204 " --> pdb=" O THR B 174 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.587A pdb=" N PHE B 254 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 229 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 256 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 277 through 280 removed outlier: 3.814A pdb=" N GLY B 376 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.543A pdb=" N THR B 474 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE B 408 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASP B 476 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR B 410 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR B 478 " --> pdb=" O THR B 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.526A pdb=" N VAL B 434 " --> pdb=" O CYS B 456 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 727 through 731 Processing sheet with id= P, first strand: chain 'C' and resid 30 through 32 Processing sheet with id= Q, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.474A pdb=" N LYS C 193 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL C 167 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU C 195 " --> pdb=" O VAL C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 218 through 221 removed outlier: 6.479A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 249 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE C 266 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 365 through 367 Processing sheet with id= T, first strand: chain 'C' and resid 399 through 402 removed outlier: 6.318A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.629A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 487 through 489 Processing sheet with id= W, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.639A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 68 through 73 removed outlier: 6.351A pdb=" N GLY D 97 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET D 39 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL D 99 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE D 100 " --> pdb=" O PRO D 123 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU D 125 " --> pdb=" O PHE D 100 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 204 through 206 removed outlier: 6.691A pdb=" N PHE D 254 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU D 229 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE D 256 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 277 through 280 removed outlier: 3.683A pdb=" N GLY D 376 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.584A pdb=" N THR D 474 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE D 408 " --> pdb=" O THR D 474 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP D 476 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR D 410 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR D 478 " --> pdb=" O THR D 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 418 through 420 Processing sheet with id= AC, first strand: chain 'D' and resid 487 through 489 Processing sheet with id= AD, first strand: chain 'D' and resid 728 through 731 removed outlier: 3.554A pdb=" N VAL D 537 " --> pdb=" O VAL D 748 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2445 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: 7.30 Time building geometry restraints manager: 9.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6998 1.34 - 1.46: 4846 1.46 - 1.58: 10271 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 22265 Sorted by residual: bond pdb=" C8 JC9 D 905 " pdb="CL1 JC9 D 905 " ideal model delta sigma weight residual 1.785 1.726 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" C5 JC9 D 905 " pdb=" O1 JC9 D 905 " ideal model delta sigma weight residual 1.184 1.232 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C ARG D 672 " pdb=" O ARG D 672 " ideal model delta sigma weight residual 1.246 1.230 0.016 9.20e-03 1.18e+04 3.03e+00 bond pdb=" CA THR A 683 " pdb=" C THR A 683 " ideal model delta sigma weight residual 1.530 1.550 -0.019 1.12e-02 7.97e+03 2.95e+00 bond pdb=" CA PRO A 304 " pdb=" C PRO A 304 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.70e-03 2.23e+04 2.92e+00 ... (remaining 22260 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 449 105.45 - 112.61: 12289 112.61 - 119.76: 6389 119.76 - 126.91: 11153 126.91 - 134.06: 314 Bond angle restraints: 30594 Sorted by residual: angle pdb=" C SER B 677 " pdb=" N PRO B 678 " pdb=" CA PRO B 678 " ideal model delta sigma weight residual 119.66 125.37 -5.71 7.20e-01 1.93e+00 6.30e+01 angle pdb=" C TRP B 390 " pdb=" N PRO B 391 " pdb=" CA PRO B 391 " ideal model delta sigma weight residual 119.28 127.84 -8.56 1.10e+00 8.26e-01 6.05e+01 angle pdb=" N ILE B 127 " pdb=" CA ILE B 127 " pdb=" C ILE B 127 " ideal model delta sigma weight residual 110.72 117.61 -6.89 1.01e+00 9.80e-01 4.65e+01 angle pdb=" N LEU B 334 " pdb=" CA LEU B 334 " pdb=" C LEU B 334 " ideal model delta sigma weight residual 113.02 120.78 -7.76 1.20e+00 6.94e-01 4.18e+01 angle pdb=" CA ASP D 675 " pdb=" C ASP D 675 " pdb=" N TYR D 676 " ideal model delta sigma weight residual 119.52 115.35 4.17 7.90e-01 1.60e+00 2.78e+01 ... (remaining 30589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 12488 22.35 - 44.70: 569 44.70 - 67.05: 110 67.05 - 89.40: 12 89.40 - 111.75: 6 Dihedral angle restraints: 13185 sinusoidal: 4124 harmonic: 9061 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 175.65 -82.65 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 16.23 76.77 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 30.61 62.39 1 1.00e+01 1.00e-02 5.15e+01 ... (remaining 13182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.068: 3792 1.068 - 2.137: 0 2.137 - 3.205: 0 3.205 - 4.273: 0 4.273 - 5.341: 1 Chirality restraints: 3793 Sorted by residual: chirality pdb=" C1 JC9 D 905 " pdb=" C2 JC9 D 905 " pdb=" C5 JC9 D 905 " pdb=" C7 JC9 D 905 " both_signs ideal model delta sigma weight residual False 2.73 -2.61 5.34 2.00e-01 2.50e+01 7.13e+02 chirality pdb=" C1 NAG A 908 " pdb=" ND2 ASN A 471 " pdb=" C2 NAG A 908 " pdb=" O5 NAG A 908 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 3790 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 907 " -0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C 907 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 907 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG C 907 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C 907 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 906 " -0.321 2.00e-02 2.50e+03 2.74e-01 9.35e+02 pdb=" C7 NAG A 906 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 906 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A 906 " 0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 906 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " 0.170 2.00e-02 2.50e+03 1.40e-01 2.46e+02 pdb=" C7 NAG A 901 " -0.047 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " 0.125 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " -0.226 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.022 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 798 2.72 - 3.26: 22886 3.26 - 3.81: 35524 3.81 - 4.35: 39807 4.35 - 4.90: 69589 Nonbonded interactions: 168604 Sorted by model distance: nonbonded pdb=" CB SER B 677 " pdb=" CD PRO B 678 " model vdw 2.172 3.840 nonbonded pdb=" O PHE D 115 " pdb=" OG SER D 118 " model vdw 2.248 2.440 nonbonded pdb=" O SER A 126 " pdb=" OG SER A 129 " model vdw 2.270 2.440 nonbonded pdb=" O MET B 133 " pdb=" NE2 GLN B 146 " model vdw 2.273 2.520 nonbonded pdb=" CG2 ILE C 83 " pdb=" O ARG C 306 " model vdw 2.274 3.460 ... (remaining 168599 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 25 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 or (resid 43 through 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 or (resid 47 through 49 and ( \ name N or name CA or name C or name O or name CB )) or resid 50 through 73 or (r \ esid 74 through 75 and (name N or name CA or name C or name O or name CB )) or r \ esid 76 through 93 or (resid 94 and (name N or name CA or name C or name O or na \ me CB )) or resid 95 through 152 or (resid 153 and (name N or name CA or name C \ or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 through 208 or (resid 209 t \ hrough 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or (resid 233 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 274 or (resid 275 and (name N or name CA or \ name C or name O or name CB )) or resid 276 through 353 or (resid 354 and (name \ N or name CA or name C or name O or name CB )) or resid 355 through 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 392 or (resid 393 through 394 and (name N or name CA or name C or name O or \ name CB )) or resid 395 through 421 or (resid 422 through 423 and (name N or na \ me CA or name C or name O or name CB )) or resid 424 through 488 or (resid 489 a \ nd (name N or name CA or name C or name O or name CB )) or resid 490 through 542 \ or (resid 543 and (name N or name CA or name C or name O or name CB )) or resid \ 544 through 550 or (resid 551 through 556 and (name N or name CA or name C or n \ ame O or name CB )) or resid 557 through 572 or (resid 573 through 577 and (name \ N or name CA or name C or name O or name CB )) or resid 578 or (resid 579 throu \ gh 582 and (name N or name CA or name C or name O or name CB )) or resid 602 or \ (resid 603 through 607 and (name N or name CA or name C or name O or name CB )) \ or resid 608 through 625 or (resid 626 through 632 and (name N or name CA or nam \ e C or name O or name CB )) or resid 633 through 653 or (resid 654 through 659 a \ nd (name N or name CA or name C or name O or name CB )) or resid 660 through 661 \ or (resid 662 and (name N or name CA or name C or name O or name CB )) or resid \ 663 through 670 or (resid 671 and (name N or name CA or name C or name O or nam \ e CB )) or resid 672 through 675 or (resid 676 through 678 and (name N or name C \ A or name C or name O or name CB )) or resid 679 through 684 or (resid 685 throu \ gh 686 and (name N or name CA or name C or name O or name CB )) or resid 687 thr \ ough 693 or (resid 694 through 699 and (name N or name CA or name C or name O or \ name CB )) or resid 700 through 726 or (resid 727 through 728 and (name N or na \ me CA or name C or name O or name CB )) or resid 729 through 731 or (resid 732 a \ nd (name N or name CA or name C or name O or name CB )) or resid 733 through 780 \ or (resid 781 and (name N or name CA or name C or name O or name CB )) or resid \ 782 through 786 or (resid 787 and (name N or name CA or name C or name O or nam \ e CB )) or resid 788 through 789 or (resid 790 and (name N or name CA or name C \ or name O or name CB )) or resid 791 through 817 or (resid 818 through 821 and ( \ name N or name CA or name C or name O or name CB )) or (resid 822 through 829 an \ d (name N or name CA or name C or name O or name CB )) or resid 830 or (resid 83 \ 1 through 841 and (name N or name CA or name C or name O or name CB )) or resid \ 901 through 910)) selection = (chain 'C' and (resid 25 through 447 or (resid 448 through 449 and (name N or na \ me CA or name C or name O or name CB )) or resid 450 through 494 or (resid 495 t \ hrough 497 and (name N or name CA or name C or name O or name CB )) or resid 498 \ through 501 or (resid 502 and (name N or name CA or name C or name O or name CB \ )) or resid 503 through 561 or (resid 562 and (name N or name CA or name C or n \ ame O or name CB )) or resid 563 through 565 or (resid 566 and (name N or name C \ A or name C or name O or name CB )) or resid 567 or (resid 568 through 569 and ( \ name N or name CA or name C or name O or name CB )) or resid 570 through 603 or \ (resid 604 through 607 and (name N or name CA or name C or name O or name CB )) \ or resid 608 through 610 or (resid 611 and (name N or name CA or name C or name \ O or name CB )) or resid 612 through 630 or (resid 631 through 632 and (name N o \ r name CA or name C or name O or name CB )) or resid 633 through 638 or (resid 6 \ 39 through 643 and (name N or name CA or name C or name O or name CB )) or resid \ 644 through 812 or (resid 813 through 814 and (name N or name CA or name C or n \ ame O or name CB )) or resid 815 through 841 or resid 901 through 910)) } ncs_group { reference = (chain 'B' and (resid 34 through 74 or (resid 75 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 90 or (resid 91 and (na \ me N or name CA or name C or name O or name CB )) or (resid 92 through 95 and (n \ ame N or name CA or name C or name O or name CB )) or resid 96 through 106 or (r \ esid 107 through 108 and (name N or name CA or name C or name O or name CB )) or \ resid 109 through 113 or (resid 114 and (name N or name CA or name C or name O \ or name CB )) or resid 115 through 116 or (resid 117 and (name N or name CA or n \ ame C or name O or name CB )) or resid 118 through 127 or (resid 128 and (name N \ or name CA or name C or name O or name CB )) or resid 129 through 132 or (resid \ 133 and (name N or name CA or name C or name O or name CB )) or resid 134 throu \ gh 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 287 or (resid 288 through 290 and (name N or name CA or name \ C or name O or name CB )) or resid 291 through 303 or (resid 304 through 306 and \ (name N or name CA or name C or name O or name CB )) or resid 307 through 309 o \ r (resid 310 through 313 and (name N or name CA or name C or name O or name CB ) \ ) or resid 314 through 318 or (resid 319 and (name N or name CA or name C or nam \ e O or name CB )) or resid 320 or (resid 321 and (name N or name CA or name C or \ name O or name CB )) or resid 322 through 332 or (resid 333 through 334 and (na \ me N or name CA or name C or name O or name CB )) or resid 335 through 337 or (r \ esid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 t \ hrough 345 or (resid 346 and (name N or name CA or name C or name O or name CB ) \ ) or resid 347 through 372 or (resid 373 and (name N or name CA or name C or nam \ e O or name CB )) or resid 374 through 393 or (resid 394 through 395 and (name N \ or name CA or name C or name O or name CB )) or resid 396 through 398 or (resid \ 399 through 400 and (name N or name CA or name C or name O or name CB )) or res \ id 401 or (resid 402 through 404 and (name N or name CA or name C or name O or n \ ame CB )) or resid 405 through 468 or (resid 469 through 470 and (name N or name \ CA or name C or name O or name CB )) or resid 471 through 493 or (resid 494 and \ (name N or name CA or name C or name O or name CB )) or resid 495 through 510 o \ r (resid 511 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 12 through 522 or (resid 523 and (name N or name CA or name C or name O or name \ CB )) or resid 524 or (resid 525 and (name N or name CA or name C or name O or n \ ame CB )) or resid 526 through 537 or (resid 538 and (name N or name CA or name \ C or name O or name CB )) or resid 539 through 540 or (resid 541 and (name N or \ name CA or name C or name O or name CB )) or resid 542 through 610 or (resid 611 \ through 613 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 14 through 626 or (resid 627 through 629 and (name N or name CA or name C or nam \ e O or name CB )) or resid 630 through 638 or (resid 639 through 641 and (name N \ or name CA or name C or name O or name CB )) or resid 642 through 647 or (resid \ 648 through 651 and (name N or name CA or name C or name O or name CB )) or res \ id 652 through 660 or (resid 661 and (name N or name CA or name C or name O or n \ ame CB )) or resid 662 or (resid 663 and (name N or name CA or name C or name O \ or name CB )) or resid 664 through 666 or (resid 667 through 669 and (name N or \ name CA or name C or name O or name CB )) or resid 670 through 683 or (resid 684 \ through 685 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 86 through 688 or (resid 689 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 705 or (resid 706 through 707 and (name N \ or name CA or name C or name O or name CB )) or resid 708 through 724 or (resid \ 725 through 727 and (name N or name CA or name C or name O or name CB )) or res \ id 728 through 753 or (resid 754 through 757 and (name N or name CA or name C or \ name O or name CB )) or resid 758 through 820 or (resid 821 through 841 and (na \ me N or name CA or name C or name O or name CB )) or resid 901 through 904)) selection = (chain 'D' and (resid 34 through 105 or (resid 106 through 108 and (name N or na \ me CA or name C or name O or name CB )) or resid 109 through 209 or (resid 210 t \ hrough 214 and (name N or name CA or name C or name O or name CB )) or resid 215 \ through 220 or (resid 221 and (name N or name CA or name C or name O or name CB \ )) or resid 222 through 311 or (resid 312 through 313 and (name N or name CA or \ name C or name O or name CB )) or resid 314 through 325 or (resid 326 and (name \ N or name CA or name C or name O or name CB )) or resid 327 through 553 or (res \ id 554 through 557 and (name N or name CA or name C or name O or name CB )) or r \ esid 558 through 563 or (resid 564 and (name N or name CA or name C or name O or \ name CB )) or resid 565 through 566 or (resid 567 and (name N or name CA or nam \ e C or name O or name CB )) or resid 568 through 575 or (resid 576 through 599 a \ nd (name N or name CA or name C or name O or name CB )) or resid 600 or (resid 6 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 602 through \ 611 or (resid 612 through 613 and (name N or name CA or name C or name O or nam \ e CB )) or resid 614 through 639 or (resid 640 through 641 and (name N or name C \ A or name C or name O or name CB )) or resid 642 through 675 or (resid 676 throu \ gh 677 and (name N or name CA or name C or name O or name CB )) or resid 678 thr \ ough 821 or (resid 822 through 841 and (name N or name CA or name C or name O or \ name CB )) or resid 901 through 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.020 Extract box with map and model: 6.730 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 60.780 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22265 Z= 0.212 Angle : 0.645 8.559 30594 Z= 0.388 Chirality : 0.099 5.341 3793 Planarity : 0.008 0.302 3868 Dihedral : 13.462 111.750 7281 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.99 % Allowed : 1.75 % Favored : 95.26 % 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: -0.02 (0.16), residues: 3102 helix: 1.63 (0.15), residues: 1273 sheet: -1.64 (0.23), residues: 467 loop : -0.97 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 198 HIS 0.005 0.000 HIS B 42 PHE 0.020 0.001 PHE C 321 TYR 0.014 0.001 TYR B 730 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 146 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8216 (ttp-110) REVERT: A 609 PHE cc_start: 0.6384 (t80) cc_final: 0.6013 (t80) REVERT: B 135 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8195 (ptm) REVERT: B 200 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8527 (tmm) REVERT: B 338 MET cc_start: 0.7898 (mmt) cc_final: 0.7590 (mmm) REVERT: C 240 MET cc_start: 0.8629 (mmt) cc_final: 0.8330 (mmp) REVERT: C 780 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8821 (t-170) REVERT: C 813 MET cc_start: 0.4433 (mmt) cc_final: 0.3209 (mtm) REVERT: D 680 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.6074 (t80) outliers start: 53 outliers final: 23 residues processed: 191 average time/residue: 0.3127 time to fit residues: 95.7707 Evaluate side-chains 160 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 198 TRP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 201 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 680 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 20.0000 chunk 236 optimal weight: 0.4980 chunk 131 optimal weight: 50.0000 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 0.0370 chunk 126 optimal weight: 0.0170 chunk 244 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 283 optimal weight: 0.7980 overall best weight: 1.0698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 650 ASN ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22265 Z= 0.149 Angle : 0.552 25.648 30594 Z= 0.265 Chirality : 0.059 2.484 3793 Planarity : 0.003 0.052 3868 Dihedral : 7.691 107.246 3848 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 1.41 % Allowed : 7.51 % Favored : 91.08 % 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: 0.04 (0.16), residues: 3102 helix: 1.71 (0.15), residues: 1277 sheet: -1.61 (0.23), residues: 480 loop : -0.97 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 390 HIS 0.010 0.001 HIS B 485 PHE 0.020 0.001 PHE D 613 TYR 0.010 0.001 TYR B 730 ARG 0.005 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: A 609 PHE cc_start: 0.6292 (t80) cc_final: 0.6008 (t80) REVERT: C 155 MET cc_start: 0.8167 (mmp) cc_final: 0.7957 (tpp) REVERT: C 240 MET cc_start: 0.8571 (mmt) cc_final: 0.8287 (mmp) REVERT: C 470 MET cc_start: 0.8855 (ttm) cc_final: 0.8584 (ttm) REVERT: C 813 MET cc_start: 0.4522 (mmt) cc_final: 0.3437 (mtm) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.2816 time to fit residues: 74.1186 Evaluate side-chains 143 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 235 optimal weight: 40.0000 chunk 192 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 281 optimal weight: 0.0030 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22265 Z= 0.185 Angle : 0.529 25.354 30594 Z= 0.254 Chirality : 0.057 2.422 3793 Planarity : 0.003 0.073 3868 Dihedral : 6.357 107.070 3798 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 1.13 % Allowed : 10.28 % Favored : 88.59 % 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: 0.13 (0.16), residues: 3102 helix: 1.83 (0.15), residues: 1276 sheet: -1.56 (0.23), residues: 476 loop : -0.97 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.005 0.001 HIS A 67 PHE 0.017 0.001 PHE B 524 TYR 0.010 0.001 TYR C 795 ARG 0.004 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 2.617 Fit side-chains REVERT: A 609 PHE cc_start: 0.6305 (t80) cc_final: 0.5990 (t80) REVERT: C 79 CYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6862 (t) REVERT: C 240 MET cc_start: 0.8607 (mmt) cc_final: 0.8324 (mmp) REVERT: C 470 MET cc_start: 0.8887 (ttm) cc_final: 0.8549 (ttm) REVERT: C 813 MET cc_start: 0.4513 (mmt) cc_final: 0.3039 (mtm) outliers start: 20 outliers final: 13 residues processed: 147 average time/residue: 0.2563 time to fit residues: 66.2488 Evaluate side-chains 142 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 676 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 6.9990 chunk 213 optimal weight: 0.0030 chunk 147 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 81 optimal weight: 30.0000 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 HIS ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 22265 Z= 0.409 Angle : 0.627 25.980 30594 Z= 0.308 Chirality : 0.059 2.386 3793 Planarity : 0.004 0.065 3868 Dihedral : 6.473 105.014 3791 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 1.92 % Allowed : 11.74 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 3102 helix: 1.63 (0.15), residues: 1280 sheet: -1.79 (0.23), residues: 471 loop : -1.11 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 634 HIS 0.007 0.001 HIS A 67 PHE 0.036 0.002 PHE D 524 TYR 0.018 0.002 TYR C 795 ARG 0.003 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 2.585 Fit side-chains REVERT: A 74 MET cc_start: 0.9179 (tmm) cc_final: 0.8428 (tmm) REVERT: A 609 PHE cc_start: 0.6323 (t80) cc_final: 0.5983 (t80) REVERT: B 518 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7367 (mpt90) REVERT: C 79 CYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6837 (t) REVERT: C 240 MET cc_start: 0.8708 (mmt) cc_final: 0.8380 (mmp) REVERT: C 470 MET cc_start: 0.9007 (ttm) cc_final: 0.8543 (ttm) REVERT: C 813 MET cc_start: 0.4470 (mmt) cc_final: 0.3399 (mtm) outliers start: 34 outliers final: 22 residues processed: 158 average time/residue: 0.2634 time to fit residues: 72.5595 Evaluate side-chains 148 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 676 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 208 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22265 Z= 0.219 Angle : 0.549 25.623 30594 Z= 0.264 Chirality : 0.057 2.385 3793 Planarity : 0.003 0.060 3868 Dihedral : 5.996 102.917 3791 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 1.47 % Allowed : 13.38 % Favored : 85.15 % 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: -0.01 (0.16), residues: 3102 helix: 1.75 (0.15), residues: 1279 sheet: -1.65 (0.23), residues: 461 loop : -1.10 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 634 HIS 0.005 0.001 HIS D 119 PHE 0.025 0.001 PHE D 524 TYR 0.011 0.001 TYR B 478 ARG 0.003 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 2.661 Fit side-chains REVERT: A 74 MET cc_start: 0.9186 (tmm) cc_final: 0.8401 (tmm) REVERT: A 609 PHE cc_start: 0.6303 (t80) cc_final: 0.5941 (t80) REVERT: C 79 CYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6807 (t) REVERT: C 240 MET cc_start: 0.8641 (mmt) cc_final: 0.8299 (mmp) REVERT: C 813 MET cc_start: 0.4321 (mmt) cc_final: 0.3361 (mtm) outliers start: 26 outliers final: 17 residues processed: 149 average time/residue: 0.2599 time to fit residues: 69.1852 Evaluate side-chains 142 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 676 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 59 optimal weight: 30.0000 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22265 Z= 0.437 Angle : 0.634 26.076 30594 Z= 0.310 Chirality : 0.059 2.376 3793 Planarity : 0.003 0.055 3868 Dihedral : 6.136 102.926 3785 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.45 % Favored : 92.52 % Rotamer: Outliers : 1.98 % Allowed : 13.95 % Favored : 84.08 % 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: -0.20 (0.16), residues: 3102 helix: 1.63 (0.15), residues: 1276 sheet: -1.90 (0.22), residues: 474 loop : -1.17 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 634 HIS 0.006 0.001 HIS B 119 PHE 0.044 0.002 PHE D 524 TYR 0.016 0.001 TYR C 795 ARG 0.003 0.000 ARG D 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 2.803 Fit side-chains REVERT: A 609 PHE cc_start: 0.6285 (t80) cc_final: 0.5909 (t80) REVERT: B 518 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7559 (mpt90) REVERT: B 524 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7969 (p90) REVERT: C 79 CYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6791 (t) REVERT: C 240 MET cc_start: 0.8731 (mmt) cc_final: 0.8350 (mmp) REVERT: C 470 MET cc_start: 0.8955 (ttm) cc_final: 0.8520 (ttm) REVERT: C 502 MET cc_start: 0.9097 (mmm) cc_final: 0.8852 (mmt) REVERT: C 813 MET cc_start: 0.4415 (mmt) cc_final: 0.3509 (mtm) outliers start: 35 outliers final: 20 residues processed: 154 average time/residue: 0.2612 time to fit residues: 71.1801 Evaluate side-chains 146 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 518 ARG Chi-restraints excluded: chain B residue 524 PHE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 676 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 30.0000 chunk 34 optimal weight: 0.0670 chunk 171 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 138 optimal weight: 50.0000 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22265 Z= 0.136 Angle : 0.536 25.308 30594 Z= 0.256 Chirality : 0.057 2.386 3793 Planarity : 0.003 0.052 3868 Dihedral : 5.596 99.134 3785 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 1.58 % Allowed : 14.96 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 3102 helix: 1.87 (0.15), residues: 1269 sheet: -1.79 (0.23), residues: 483 loop : -1.03 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 634 HIS 0.006 0.001 HIS B 42 PHE 0.015 0.001 PHE D 170 TYR 0.010 0.001 TYR B 478 ARG 0.002 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 2.584 Fit side-chains REVERT: A 609 PHE cc_start: 0.6205 (t80) cc_final: 0.5854 (t80) REVERT: C 79 CYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6743 (t) REVERT: C 240 MET cc_start: 0.8603 (mmt) cc_final: 0.8284 (mmp) REVERT: C 470 MET cc_start: 0.8815 (ttm) cc_final: 0.8406 (ttm) REVERT: C 813 MET cc_start: 0.4379 (mmt) cc_final: 0.3502 (mtm) REVERT: D 507 MET cc_start: 0.8349 (ttm) cc_final: 0.8148 (ttm) outliers start: 28 outliers final: 15 residues processed: 152 average time/residue: 0.2617 time to fit residues: 69.5698 Evaluate side-chains 140 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 236 optimal weight: 0.0030 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22265 Z= 0.285 Angle : 0.571 25.755 30594 Z= 0.274 Chirality : 0.058 2.380 3793 Planarity : 0.003 0.047 3868 Dihedral : 5.665 96.698 3785 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.19 % Favored : 93.78 % Rotamer: Outliers : 1.36 % Allowed : 15.13 % Favored : 83.51 % 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: -0.01 (0.16), residues: 3102 helix: 1.81 (0.15), residues: 1277 sheet: -1.78 (0.23), residues: 487 loop : -1.08 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 634 HIS 0.005 0.001 HIS D 119 PHE 0.030 0.001 PHE D 524 TYR 0.013 0.001 TYR D 286 ARG 0.002 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 2.796 Fit side-chains REVERT: A 609 PHE cc_start: 0.6214 (t80) cc_final: 0.5856 (t80) REVERT: C 79 CYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6740 (t) REVERT: C 240 MET cc_start: 0.8683 (mmt) cc_final: 0.8337 (mmp) REVERT: C 470 MET cc_start: 0.8933 (ttm) cc_final: 0.8501 (ttm) REVERT: C 813 MET cc_start: 0.4511 (mmt) cc_final: 0.3390 (mtm) outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 0.2562 time to fit residues: 67.6973 Evaluate side-chains 147 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 748 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 20.0000 chunk 288 optimal weight: 5.9990 chunk 262 optimal weight: 0.0770 chunk 280 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22265 Z= 0.187 Angle : 0.542 25.392 30594 Z= 0.257 Chirality : 0.057 2.392 3793 Planarity : 0.003 0.045 3868 Dihedral : 5.411 90.234 3785 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 1.30 % Allowed : 15.19 % Favored : 83.51 % 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: 0.10 (0.16), residues: 3102 helix: 1.90 (0.15), residues: 1280 sheet: -1.72 (0.23), residues: 489 loop : -1.02 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 634 HIS 0.005 0.001 HIS B 42 PHE 0.019 0.001 PHE D 170 TYR 0.011 0.001 TYR B 478 ARG 0.003 0.000 ARG B 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 2.596 Fit side-chains REVERT: A 609 PHE cc_start: 0.6213 (t80) cc_final: 0.5851 (t80) REVERT: C 79 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6725 (t) REVERT: C 240 MET cc_start: 0.8636 (mmt) cc_final: 0.8318 (mmp) REVERT: C 470 MET cc_start: 0.8853 (ttm) cc_final: 0.8395 (ttm) REVERT: C 813 MET cc_start: 0.4443 (mmt) cc_final: 0.3395 (mtm) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.2540 time to fit residues: 66.9953 Evaluate side-chains 147 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 9.9990 chunk 296 optimal weight: 0.0970 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 286 optimal weight: 40.0000 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 191 optimal weight: 0.0270 chunk 151 optimal weight: 8.9990 overall best weight: 3.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22265 Z= 0.284 Angle : 0.575 25.617 30594 Z= 0.275 Chirality : 0.058 2.398 3793 Planarity : 0.003 0.043 3868 Dihedral : 5.510 83.104 3785 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 1.52 % Allowed : 15.08 % Favored : 83.40 % 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: 0.06 (0.16), residues: 3102 helix: 1.86 (0.15), residues: 1282 sheet: -1.67 (0.23), residues: 484 loop : -1.08 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 634 HIS 0.005 0.001 HIS D 119 PHE 0.029 0.001 PHE D 524 TYR 0.012 0.001 TYR D 286 ARG 0.002 0.000 ARG B 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6204 Ramachandran restraints generated. 3102 Oldfield, 0 Emsley, 3102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.701 Fit side-chains REVERT: A 609 PHE cc_start: 0.6221 (t80) cc_final: 0.5876 (t80) REVERT: C 79 CYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6710 (t) REVERT: C 240 MET cc_start: 0.8691 (mmt) cc_final: 0.8353 (mmp) REVERT: C 470 MET cc_start: 0.8944 (ttm) cc_final: 0.8489 (ttm) REVERT: C 813 MET cc_start: 0.4448 (mmt) cc_final: 0.3411 (mtm) outliers start: 27 outliers final: 24 residues processed: 150 average time/residue: 0.2599 time to fit residues: 69.3100 Evaluate side-chains 150 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 HIS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 198 TRP Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 676 TYR Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 748 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 7.9990 chunk 263 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 254 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 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 = 0.3665 r_free = 0.3665 target = 0.076472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054197 restraints weight = 82117.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.056316 restraints weight = 47021.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056287 restraints weight = 29949.401| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22265 Z= 0.163 Angle : 0.538 25.200 30594 Z= 0.254 Chirality : 0.057 2.412 3793 Planarity : 0.003 0.041 3868 Dihedral : 5.136 77.904 3785 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 1.30 % Allowed : 15.47 % Favored : 83.23 % 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: 0.18 (0.16), residues: 3102 helix: 1.96 (0.15), residues: 1276 sheet: -1.65 (0.23), residues: 487 loop : -0.99 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 634 HIS 0.005 0.001 HIS B 42 PHE 0.020 0.001 PHE D 170 TYR 0.010 0.001 TYR B 478 ARG 0.002 0.000 ARG C 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.47 seconds wall clock time: 61 minutes 18.06 seconds (3678.06 seconds total)