Starting phenix.real_space_refine on Sat Jul 4 01:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szg_40915/07_2026/8szg_40915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szg_40915/07_2026/8szg_40915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8szg_40915/07_2026/8szg_40915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szg_40915/07_2026/8szg_40915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szg_40915/07_2026/8szg_40915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szg_40915/07_2026/8szg_40915.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.048 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 3 5.49 5 S 100 5.16 5 C 11359 2.51 5 N 2904 2.21 5 O 3196 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17571 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2404 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 6, 'ARG:plan': 6, 'ASP:plan': 11, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 368 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 6520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6520 Classifications: {'peptide': 830} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 32, 'TRANS': 797} Chain breaks: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 8, 'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "B" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6279 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 31, 'TRANS': 764} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 6, 'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 130 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 156 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1208 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 6} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 117 Unusual residues: {'CLR': 1, 'NAG': 2, 'PO4': 1, 'SPM': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1405 "'] Classifications: {'peptide': 1, 'undetermined': 6, 'water': 1} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.27, per 1000 atoms: 0.19 Number of scatterers: 17571 At special positions: 0 Unit cell: (102.389, 108.463, 251.633, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 100 16.00 P 3 15.00 F 6 9.00 O 3196 8.00 N 2904 7.00 C 11359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1202 " - " ASN A 287 " " NAG A1203 " - " ASN A 468 " " NAG B1402 " - " ASN B 468 " " NAG B1403 " - " ASN B 488 " " NAG F 1 " - " ASN A 488 " " NAG G 1 " - " ASN A 541 " " NAG H 1 " - " ASN B 541 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 554.5 milliseconds 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4216 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 24 sheets defined 43.5% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.703A pdb=" N ALA D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.647A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.626A pdb=" N HIS E 44 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.757A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.614A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.929A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.749A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.659A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.513A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.978A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 4.458A pdb=" N HIS A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.831A pdb=" N PHE A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.758A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 451 through 455 removed outlier: 4.193A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.522A pdb=" N VAL A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.862A pdb=" N LEU A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.561A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 4.039A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) 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 673 through 706 removed outlier: 5.064A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix Processing helix chain 'A' and resid 716 through 746 removed outlier: 3.606A pdb=" N LEU A 723 " --> pdb=" O TRP A 719 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.515A pdb=" N GLY A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 removed outlier: 3.565A pdb=" N LEU A 812 " --> pdb=" O THR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 removed outlier: 3.550A pdb=" N TYR A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 863 removed outlier: 3.844A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 867 Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.886A pdb=" N VAL A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.562A pdb=" N PHE B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.596A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.885A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.699A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.543A pdb=" N LEU B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.912A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.524A pdb=" N SER B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.568A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 416 through 436 removed outlier: 3.544A pdb=" N VAL B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.547A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.557A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.855A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 666 removed outlier: 3.579A pdb=" N PHE B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 673 through 698 removed outlier: 3.647A pdb=" N CYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix removed outlier: 3.512A pdb=" N ILE B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.514A pdb=" N PHE B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.774A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.688A pdb=" N ALA B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 removed outlier: 3.901A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 832 through 862 removed outlier: 3.606A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.539A pdb=" N GLN C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 233 through 236 removed outlier: 4.000A pdb=" N ASP C 236 " --> pdb=" O SER C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 246 through 261 removed outlier: 3.753A pdb=" N GLU C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 261 " --> pdb=" O THR C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 removed outlier: 4.004A pdb=" N LEU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.577A pdb=" N TYR C 291 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.767A pdb=" N LEU C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 356 Processing sheet with id=AA1, first strand: chain 'D' and resid 46 through 51 removed outlier: 6.351A pdb=" N THR D 47 " --> pdb=" O ASN D 340 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN D 340 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG D 49 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 337 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.945A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 72 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 80 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER D 74 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS D 91 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.590A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 148 through 151 removed outlier: 3.804A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 178 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.660A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 201 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 209 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.751A pdb=" N ALA D 231 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 253 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 251 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 252 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 278 removed outlier: 4.194A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL D 296 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.493A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 142 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 236 through 243 removed outlier: 8.194A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 269 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.872A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.636A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB4, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'A' and resid 589 through 590 Processing sheet with id=AB6, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.189A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.635A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 142 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 236 through 243 removed outlier: 8.051A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC2, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'B' and resid 602 through 604 removed outlier: 6.614A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 749 through 750 removed outlier: 3.786A pdb=" N SER B 749 " --> pdb=" O HIS B 766 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.648A pdb=" N LEU C 40 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 225 through 231 removed outlier: 5.970A pdb=" N ILE C 226 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 272 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 228 " --> pdb=" O PHE C 272 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN C 274 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 230 " --> pdb=" O ASN C 274 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2106 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: 2.70 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2955 1.32 - 1.46: 5579 1.46 - 1.59: 9309 1.59 - 1.72: 6 1.72 - 1.86: 127 Bond restraints: 17976 Sorted by residual: bond pdb=" C31 PCW A1204 " pdb=" O2 PCW A1204 " ideal model delta sigma weight residual 1.333 1.487 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" CG1 ILE C 337 " pdb=" CD1 ILE C 337 " ideal model delta sigma weight residual 1.513 1.267 0.246 3.90e-02 6.57e+02 3.96e+01 bond pdb=" C16 PCW A1204 " pdb=" C17 PCW A1204 " ideal model delta sigma weight residual 1.523 1.623 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C31 PCW A1204 " pdb=" C32 PCW A1204 " ideal model delta sigma weight residual 1.502 1.601 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C11 PCW A1204 " pdb=" O3 PCW A1204 " ideal model delta sigma weight residual 1.326 1.417 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 17971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 24318 4.95 - 9.90: 75 9.90 - 14.84: 5 14.84 - 19.79: 1 19.79 - 24.74: 2 Bond angle restraints: 24401 Sorted by residual: angle pdb=" C PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta sigma weight residual 110.85 88.88 21.97 1.70e+00 3.46e-01 1.67e+02 angle pdb=" C18 PCW A1204 " pdb=" C19 PCW A1204 " pdb=" C20 PCW A1204 " ideal model delta sigma weight residual 127.82 152.56 -24.74 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C THR B 596 " pdb=" CA THR B 596 " pdb=" CB THR B 596 " ideal model delta sigma weight residual 110.88 98.18 12.70 1.57e+00 4.06e-01 6.54e+01 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 111.07 103.21 7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N ILE B 434 " pdb=" CA ILE B 434 " pdb=" C ILE B 434 " ideal model delta sigma weight residual 110.72 103.40 7.32 1.01e+00 9.80e-01 5.25e+01 ... (remaining 24396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 10481 32.59 - 65.17: 266 65.17 - 97.76: 25 97.76 - 130.34: 1 130.34 - 162.93: 1 Dihedral angle restraints: 10774 sinusoidal: 4269 harmonic: 6505 Sorted by residual: dihedral pdb=" C PHE C 341 " pdb=" N PHE C 341 " pdb=" CA PHE C 341 " pdb=" CB PHE C 341 " ideal model delta harmonic sigma weight residual -122.60 -95.83 -26.77 0 2.50e+00 1.60e-01 1.15e+02 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual -86.00 -176.09 90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -169.45 83.45 1 1.00e+01 1.00e-02 8.50e+01 ... (remaining 10771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.027: 2785 1.027 - 2.053: 0 2.053 - 3.080: 0 3.080 - 4.107: 0 4.107 - 5.133: 1 Chirality restraints: 2786 Sorted by residual: chirality pdb=" C2 PCW A1204 " pdb=" C1 PCW A1204 " pdb=" C3 PCW A1204 " pdb=" O2 PCW A1204 " both_signs ideal model delta sigma weight residual False -2.32 2.81 -5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA ASP C 346 " pdb=" N ASP C 346 " pdb=" C ASP C 346 " pdb=" CB ASP C 346 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.48e+01 ... (remaining 2783 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 821 " -0.044 2.00e-02 2.50e+03 4.41e-02 3.40e+01 pdb=" CG PHE B 821 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE B 821 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE B 821 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE B 821 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE B 821 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 821 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 792 " 0.030 2.00e-02 2.50e+03 3.97e-02 2.75e+01 pdb=" CG PHE B 792 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 792 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE B 792 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE B 792 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE B 792 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 792 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 712 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C THR A 712 " -0.073 2.00e-02 2.50e+03 pdb=" O THR A 712 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 713 " 0.024 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4758 2.80 - 3.33: 15600 3.33 - 3.85: 26727 3.85 - 4.38: 30397 4.38 - 4.90: 53679 Nonbonded interactions: 131161 Sorted by model distance: nonbonded pdb=" OG1 THR B 550 " pdb=" O VAL B 566 " model vdw 2.281 3.040 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR D 102 " pdb=" O SER D 147 " model vdw 2.308 3.040 nonbonded pdb=" OE1 GLU B 229 " pdb=" NH1 ARG B 233 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG B 69 " pdb=" O2 PO4 B1406 " model vdw 2.326 3.120 ... (remaining 131156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 118 or (resid 119 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 546 or (resid 547 through 548 and (name N \ or name CA or name C or name O or name CB )) or resid 549 through 586 or (resid \ 587 through 588 and (name N or name CA or name C or name O or name CB )) or resi \ d 589 through 673 or (resid 674 and (name N or name CA or name C or name O or na \ me CB )) or resid 675 through 707 or resid 722 through 734 or (resid 735 and (na \ me N or name CA or name C or name O or name CB )) or resid 736 through 756 or (r \ esid 757 and (name N or name CA or name C or name O or name CB )) or resid 758 t \ hrough 801 or (resid 802 and (name N or name CA or name C or name O or name CB ) \ ) or resid 803 through 868 or (resid 869 through 871 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1208 through 1209)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 120 or (resid 134 through 135 and \ (name N or name CA or name C or name O or name CB )) or resid 136 through 360 or \ (resid 361 through 362 and (name N or name CA or name C or name O or name CB )) \ or resid 392 through 480 or (resid 481 and (name N or name CA or name C or name \ O or name CB )) or resid 482 through 498 or (resid 499 through 500 and (name N \ or name CA or name C or name O or name CB )) or resid 501 through 591 or (resid \ 592 through 593 and (name N or name CA or name C or name O or name CB )) or resi \ d 594 through 608 or (resid 609 through 610 and (name N or name CA or name C or \ name O or name CB )) or resid 611 through 670 or (resid 671 and (name N or name \ CA or name C or name O or name CB )) or resid 672 through 706 or (resid 707 thro \ ugh 722 and (name N or name CA or name C or name O or name CB )) or resid 723 th \ rough 871 or resid 1405 through 1406)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 9.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.040 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.006 0.246 18004 Z= 0.343 Angle : 0.853 24.740 24467 Z= 0.519 Chirality : 0.114 5.133 2786 Planarity : 0.005 0.050 3061 Dihedral : 14.080 162.926 6504 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 2209 helix: 0.79 (0.18), residues: 869 sheet: -0.76 (0.29), residues: 347 loop : -1.25 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 701 TYR 0.031 0.002 TYR B 829 PHE 0.085 0.003 PHE B 821 TRP 0.023 0.002 TRP B 742 HIS 0.010 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.34 (17976) covalent geometry : angle 0.85083 / 0.52 (24401) SS BOND : bond 0.00241 / 0.17 ( 18) SS BOND : angle 1.60138 / 1.20 ( 36) hydrogen bonds : bond 0.19316 / 13.58 ( 732) hydrogen bonds : angle 6.38958 / 4.51 ( 2106) link_BETA1-4 : bond 0.00536 / 0.26 ( 3) link_BETA1-4 : angle 1.21680 / 0.73 ( 9) link_NAG-ASN : bond 0.00146 / 0.10 ( 7) link_NAG-ASN : angle 1.50539 / 0.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8753 (mppt) cc_final: 0.8404 (mmtm) REVERT: D 63 TRP cc_start: 0.7781 (m100) cc_final: 0.7371 (m100) REVERT: A 790 PHE cc_start: 0.8329 (m-10) cc_final: 0.7984 (m-80) REVERT: A 832 PHE cc_start: 0.6995 (m-10) cc_final: 0.6712 (m-80) REVERT: B 510 TYR cc_start: 0.8072 (p90) cc_final: 0.7869 (p90) REVERT: B 558 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7596 (mm-30) REVERT: B 618 LEU cc_start: 0.7929 (mt) cc_final: 0.7534 (pp) REVERT: B 738 ILE cc_start: 0.7575 (tp) cc_final: 0.7297 (tt) REVERT: C 29 LEU cc_start: 0.8964 (tp) cc_final: 0.8689 (tt) REVERT: C 44 LEU cc_start: 0.7931 (tp) cc_final: 0.7509 (tp) REVERT: C 259 ILE cc_start: 0.8241 (mm) cc_final: 0.7754 (tt) REVERT: C 282 LYS cc_start: 0.7408 (mtpt) cc_final: 0.7189 (mtpp) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.1222 time to fit residues: 56.1221 Evaluate side-chains 240 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 471 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.087976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071911 restraints weight = 49704.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072002 restraints weight = 42850.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072659 restraints weight = 37750.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073000 restraints weight = 30322.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073145 restraints weight = 29843.924| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18004 Z= 0.139 Angle : 0.568 9.462 24467 Z= 0.301 Chirality : 0.043 0.249 2786 Planarity : 0.004 0.043 3061 Dihedral : 8.764 83.242 2762 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.17 % Allowed : 8.44 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2209 helix: 1.34 (0.18), residues: 881 sheet: -0.63 (0.28), residues: 361 loop : -1.32 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.017 0.001 TYR D 111 PHE 0.020 0.001 PHE A 814 TRP 0.018 0.001 TRP B 818 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17976) covalent geometry : angle 0.56090 / 0.30 (24401) SS BOND : bond 0.00290 / 0.17 ( 18) SS BOND : angle 2.18907 / 1.68 ( 36) hydrogen bonds : bond 0.05941 / 4.11 ( 732) hydrogen bonds : angle 4.61679 / 3.26 ( 2106) link_BETA1-4 : bond 0.00256 / 0.13 ( 3) link_BETA1-4 : angle 1.12401 / 0.67 ( 9) link_NAG-ASN : bond 0.00193 / 0.13 ( 7) link_NAG-ASN : angle 1.38621 / 0.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8668 (mppt) cc_final: 0.8414 (mmtm) REVERT: D 63 TRP cc_start: 0.7684 (m100) cc_final: 0.7313 (m100) REVERT: A 760 ILE cc_start: 0.8648 (mt) cc_final: 0.8303 (mm) REVERT: A 790 PHE cc_start: 0.8048 (m-10) cc_final: 0.7696 (m-80) REVERT: A 829 TYR cc_start: 0.7991 (p90) cc_final: 0.7620 (p90) REVERT: A 832 PHE cc_start: 0.6988 (m-10) cc_final: 0.6697 (m-80) REVERT: B 446 ASN cc_start: 0.7757 (t0) cc_final: 0.7534 (t0) REVERT: B 558 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 848 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 852 ILE cc_start: 0.8493 (mt) cc_final: 0.8268 (mm) REVERT: C 29 LEU cc_start: 0.8814 (tp) cc_final: 0.8556 (tt) REVERT: C 259 ILE cc_start: 0.8138 (mm) cc_final: 0.7480 (pt) REVERT: C 321 ASP cc_start: 0.7058 (t0) cc_final: 0.6800 (t0) outliers start: 21 outliers final: 11 residues processed: 261 average time/residue: 0.1199 time to fit residues: 47.6392 Evaluate side-chains 241 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain B residue 848 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 47 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 800 ASN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070391 restraints weight = 49962.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070429 restraints weight = 43320.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070955 restraints weight = 39945.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071222 restraints weight = 31420.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071319 restraints weight = 29399.861| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18004 Z= 0.188 Angle : 0.582 10.591 24467 Z= 0.307 Chirality : 0.044 0.234 2786 Planarity : 0.004 0.044 3061 Dihedral : 8.436 80.103 2761 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.62 % Allowed : 11.29 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.18), residues: 2209 helix: 1.32 (0.18), residues: 881 sheet: -0.81 (0.28), residues: 365 loop : -1.38 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 873 TYR 0.015 0.002 TYR B 425 PHE 0.018 0.001 PHE A 814 TRP 0.017 0.002 TRP A 530 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (17976) covalent geometry : angle 0.57776 / 0.31 (24401) SS BOND : bond 0.00469 / 0.35 ( 18) SS BOND : angle 1.41731 / 0.98 ( 36) hydrogen bonds : bond 0.05917 / 4.11 ( 732) hydrogen bonds : angle 4.39366 / 3.08 ( 2106) link_BETA1-4 : bond 0.00325 / 0.16 ( 3) link_BETA1-4 : angle 1.28466 / 0.76 ( 9) link_NAG-ASN : bond 0.00273 / 0.21 ( 7) link_NAG-ASN : angle 1.68263 / 1.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7758 (m100) cc_final: 0.7357 (m100) REVERT: D 234 PHE cc_start: 0.5264 (t80) cc_final: 0.4903 (t80) REVERT: A 760 ILE cc_start: 0.8645 (mt) cc_final: 0.8337 (mm) REVERT: A 790 PHE cc_start: 0.8141 (m-10) cc_final: 0.7742 (m-80) REVERT: A 829 TYR cc_start: 0.8010 (p90) cc_final: 0.7734 (p90) REVERT: A 832 PHE cc_start: 0.7061 (m-10) cc_final: 0.6785 (m-80) REVERT: B 446 ASN cc_start: 0.7766 (t0) cc_final: 0.7421 (t0) REVERT: B 558 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 738 ILE cc_start: 0.7450 (tp) cc_final: 0.7126 (tt) REVERT: C 27 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7300 (ptp-170) REVERT: C 29 LEU cc_start: 0.8819 (tp) cc_final: 0.8558 (tt) REVERT: C 228 PHE cc_start: 0.7148 (t80) cc_final: 0.6947 (t80) REVERT: C 259 ILE cc_start: 0.8190 (mm) cc_final: 0.7510 (pt) REVERT: C 321 ASP cc_start: 0.7098 (t0) cc_final: 0.6880 (t0) outliers start: 29 outliers final: 20 residues processed: 245 average time/residue: 0.1282 time to fit residues: 47.8897 Evaluate side-chains 245 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 815 PHE Chi-restraints excluded: chain C residue 191 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 173 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS B 471 ASN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069154 restraints weight = 50389.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068894 restraints weight = 47910.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069624 restraints weight = 40776.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069982 restraints weight = 33361.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070110 restraints weight = 31830.528| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18004 Z= 0.217 Angle : 0.599 9.498 24467 Z= 0.316 Chirality : 0.045 0.234 2786 Planarity : 0.004 0.045 3061 Dihedral : 8.176 77.900 2761 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.01 % Allowed : 13.53 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2209 helix: 1.21 (0.18), residues: 880 sheet: -0.96 (0.28), residues: 365 loop : -1.46 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.015 0.002 TYR E 40 PHE 0.021 0.002 PHE A 625 TRP 0.019 0.002 TRP A 530 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (17976) covalent geometry : angle 0.59310 / 0.31 (24401) SS BOND : bond 0.00352 / 0.24 ( 18) SS BOND : angle 1.72221 / 1.13 ( 36) hydrogen bonds : bond 0.06078 / 4.21 ( 732) hydrogen bonds : angle 4.37274 / 3.07 ( 2106) link_BETA1-4 : bond 0.00252 / 0.13 ( 3) link_BETA1-4 : angle 1.32370 / 0.79 ( 9) link_NAG-ASN : bond 0.00346 / 0.27 ( 7) link_NAG-ASN : angle 1.86072 / 1.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7795 (m100) cc_final: 0.7383 (m100) REVERT: D 234 PHE cc_start: 0.5329 (t80) cc_final: 0.5092 (t80) REVERT: A 790 PHE cc_start: 0.8218 (m-10) cc_final: 0.7797 (m-80) REVERT: A 829 TYR cc_start: 0.7989 (p90) cc_final: 0.7719 (p90) REVERT: A 832 PHE cc_start: 0.7105 (m-10) cc_final: 0.6796 (m-80) REVERT: B 446 ASN cc_start: 0.7772 (t0) cc_final: 0.7403 (t0) REVERT: B 558 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 738 ILE cc_start: 0.7548 (tp) cc_final: 0.7257 (tt) REVERT: B 854 PHE cc_start: 0.7394 (m-80) cc_final: 0.7038 (m-80) REVERT: C 27 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7371 (ptp-170) REVERT: C 29 LEU cc_start: 0.8859 (tp) cc_final: 0.8603 (tt) REVERT: C 259 ILE cc_start: 0.8182 (mm) cc_final: 0.7518 (pt) REVERT: C 312 MET cc_start: 0.8197 (tpp) cc_final: 0.7862 (tmm) REVERT: C 321 ASP cc_start: 0.7124 (t0) cc_final: 0.6922 (t0) outliers start: 36 outliers final: 27 residues processed: 246 average time/residue: 0.1218 time to fit residues: 46.0154 Evaluate side-chains 250 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 14 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.085777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069557 restraints weight = 49989.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069252 restraints weight = 46763.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069854 restraints weight = 39975.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070123 restraints weight = 32384.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070307 restraints weight = 28744.823| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18004 Z= 0.172 Angle : 0.559 10.326 24467 Z= 0.294 Chirality : 0.044 0.233 2786 Planarity : 0.004 0.046 3061 Dihedral : 7.798 80.145 2761 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.68 % Allowed : 13.58 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2209 helix: 1.27 (0.18), residues: 878 sheet: -0.98 (0.28), residues: 365 loop : -1.45 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.015 0.001 TYR B 421 PHE 0.019 0.001 PHE B 789 TRP 0.018 0.002 TRP A 530 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (17976) covalent geometry : angle 0.55324 / 0.29 (24401) SS BOND : bond 0.00281 / 0.21 ( 18) SS BOND : angle 1.55860 / 0.98 ( 36) hydrogen bonds : bond 0.05517 / 3.81 ( 732) hydrogen bonds : angle 4.23787 / 2.98 ( 2106) link_BETA1-4 : bond 0.00327 / 0.17 ( 3) link_BETA1-4 : angle 1.22581 / 0.74 ( 9) link_NAG-ASN : bond 0.00251 / 0.20 ( 7) link_NAG-ASN : angle 1.74496 / 1.18 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7805 (m100) cc_final: 0.7408 (m100) REVERT: D 334 SER cc_start: 0.6643 (p) cc_final: 0.6213 (p) REVERT: A 790 PHE cc_start: 0.8207 (m-10) cc_final: 0.7875 (m-10) REVERT: A 829 TYR cc_start: 0.7970 (p90) cc_final: 0.7713 (p90) REVERT: A 832 PHE cc_start: 0.7098 (m-10) cc_final: 0.6789 (m-80) REVERT: B 446 ASN cc_start: 0.7782 (t0) cc_final: 0.7378 (t0) REVERT: B 558 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7705 (mm-30) REVERT: B 738 ILE cc_start: 0.7521 (tp) cc_final: 0.7310 (tp) REVERT: B 854 PHE cc_start: 0.7450 (m-80) cc_final: 0.7149 (m-80) REVERT: C 29 LEU cc_start: 0.8871 (tp) cc_final: 0.8633 (tt) REVERT: C 203 MET cc_start: 0.7201 (mmt) cc_final: 0.6881 (mmt) REVERT: C 259 ILE cc_start: 0.8146 (mm) cc_final: 0.7473 (pt) REVERT: C 321 ASP cc_start: 0.7137 (t0) cc_final: 0.6926 (t0) outliers start: 48 outliers final: 31 residues processed: 259 average time/residue: 0.1206 time to fit residues: 47.5479 Evaluate side-chains 252 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 212 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.0020 chunk 68 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN B 359 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.085874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069639 restraints weight = 50105.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069308 restraints weight = 45980.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069720 restraints weight = 40650.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070187 restraints weight = 33376.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.070239 restraints weight = 31843.601| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18004 Z= 0.167 Angle : 0.559 9.803 24467 Z= 0.295 Chirality : 0.043 0.235 2786 Planarity : 0.004 0.046 3061 Dihedral : 7.647 78.566 2761 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.46 % Allowed : 15.26 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2209 helix: 1.34 (0.18), residues: 873 sheet: -0.96 (0.28), residues: 364 loop : -1.46 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 256 TYR 0.015 0.001 TYR B 421 PHE 0.023 0.001 PHE B 789 TRP 0.017 0.002 TRP A 530 HIS 0.006 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (17976) covalent geometry : angle 0.55281 / 0.29 (24401) SS BOND : bond 0.00250 / 0.18 ( 18) SS BOND : angle 1.65987 / 1.03 ( 36) hydrogen bonds : bond 0.05406 / 3.73 ( 732) hydrogen bonds : angle 4.20796 / 2.96 ( 2106) link_BETA1-4 : bond 0.00243 / 0.12 ( 3) link_BETA1-4 : angle 1.24002 / 0.75 ( 9) link_NAG-ASN : bond 0.00248 / 0.20 ( 7) link_NAG-ASN : angle 1.72939 / 1.16 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7802 (m100) cc_final: 0.7416 (m100) REVERT: D 334 SER cc_start: 0.6641 (p) cc_final: 0.6204 (p) REVERT: E 21 MET cc_start: 0.7210 (ppp) cc_final: 0.6222 (ttp) REVERT: A 829 TYR cc_start: 0.7957 (p90) cc_final: 0.7730 (p90) REVERT: A 832 PHE cc_start: 0.7116 (m-10) cc_final: 0.6813 (m-80) REVERT: B 446 ASN cc_start: 0.7770 (t0) cc_final: 0.7343 (t0) REVERT: B 558 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 738 ILE cc_start: 0.7541 (tp) cc_final: 0.7331 (tp) REVERT: B 854 PHE cc_start: 0.7465 (m-80) cc_final: 0.7187 (m-80) REVERT: C 29 LEU cc_start: 0.8877 (tp) cc_final: 0.8637 (tt) REVERT: C 203 MET cc_start: 0.7232 (mmt) cc_final: 0.6939 (mmt) REVERT: C 228 PHE cc_start: 0.6942 (t80) cc_final: 0.6728 (t80) REVERT: C 259 ILE cc_start: 0.8135 (mm) cc_final: 0.7453 (pt) REVERT: C 306 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5881 (ptp-170) REVERT: C 312 MET cc_start: 0.8166 (tpp) cc_final: 0.7847 (tmm) REVERT: C 321 ASP cc_start: 0.7150 (t0) cc_final: 0.6943 (t0) outliers start: 44 outliers final: 34 residues processed: 251 average time/residue: 0.1170 time to fit residues: 44.9294 Evaluate side-chains 255 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 205 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN B 359 HIS B 471 ASN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.085787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069557 restraints weight = 50212.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.069357 restraints weight = 45724.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069812 restraints weight = 43155.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.070154 restraints weight = 34976.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070209 restraints weight = 33356.345| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18004 Z= 0.174 Angle : 0.567 13.222 24467 Z= 0.298 Chirality : 0.044 0.235 2786 Planarity : 0.004 0.046 3061 Dihedral : 7.494 77.198 2761 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.85 % Allowed : 15.43 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2209 helix: 1.30 (0.18), residues: 875 sheet: -0.99 (0.28), residues: 364 loop : -1.48 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.015 0.002 TYR B 421 PHE 0.032 0.001 PHE B 789 TRP 0.017 0.001 TRP A 530 HIS 0.008 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (17976) covalent geometry : angle 0.56107 / 0.30 (24401) SS BOND : bond 0.00245 / 0.17 ( 18) SS BOND : angle 1.59605 / 1.02 ( 36) hydrogen bonds : bond 0.05432 / 3.75 ( 732) hydrogen bonds : angle 4.20361 / 2.95 ( 2106) link_BETA1-4 : bond 0.00257 / 0.13 ( 3) link_BETA1-4 : angle 1.26644 / 0.77 ( 9) link_NAG-ASN : bond 0.00262 / 0.21 ( 7) link_NAG-ASN : angle 1.75983 / 1.18 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7804 (m100) cc_final: 0.7393 (m100) REVERT: D 334 SER cc_start: 0.6632 (p) cc_final: 0.6198 (p) REVERT: A 832 PHE cc_start: 0.7082 (m-10) cc_final: 0.6798 (m-80) REVERT: B 446 ASN cc_start: 0.7795 (t0) cc_final: 0.7366 (t0) REVERT: B 558 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 738 ILE cc_start: 0.7556 (tp) cc_final: 0.7348 (tp) REVERT: B 854 PHE cc_start: 0.7446 (m-80) cc_final: 0.7215 (m-80) REVERT: C 29 LEU cc_start: 0.8890 (tp) cc_final: 0.8653 (tt) REVERT: C 203 MET cc_start: 0.7288 (mmt) cc_final: 0.7016 (mmt) REVERT: C 259 ILE cc_start: 0.8107 (mm) cc_final: 0.7386 (pt) REVERT: C 312 MET cc_start: 0.8161 (tpp) cc_final: 0.7930 (tmm) outliers start: 51 outliers final: 41 residues processed: 255 average time/residue: 0.1213 time to fit residues: 46.9759 Evaluate side-chains 260 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 819 ILE Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 138 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 56 optimal weight: 0.2980 chunk 134 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 350 GLN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.086800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070604 restraints weight = 49945.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070233 restraints weight = 46498.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070964 restraints weight = 40224.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071224 restraints weight = 31538.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071267 restraints weight = 30718.373| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18004 Z= 0.117 Angle : 0.533 12.250 24467 Z= 0.279 Chirality : 0.042 0.233 2786 Planarity : 0.004 0.047 3061 Dihedral : 7.204 75.623 2761 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.07 % Allowed : 16.66 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.18), residues: 2209 helix: 1.53 (0.18), residues: 872 sheet: -0.92 (0.28), residues: 364 loop : -1.44 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 13 TYR 0.014 0.001 TYR B 744 PHE 0.029 0.001 PHE B 789 TRP 0.015 0.001 TRP A 530 HIS 0.024 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (17976) covalent geometry : angle 0.52894 / 0.28 (24401) SS BOND : bond 0.00197 / 0.15 ( 18) SS BOND : angle 1.38215 / 0.88 ( 36) hydrogen bonds : bond 0.04694 / 3.23 ( 732) hydrogen bonds : angle 4.04129 / 2.85 ( 2106) link_BETA1-4 : bond 0.00287 / 0.14 ( 3) link_BETA1-4 : angle 1.12630 / 0.69 ( 9) link_NAG-ASN : bond 0.00159 / 0.11 ( 7) link_NAG-ASN : angle 1.57143 / 1.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7815 (m100) cc_final: 0.7458 (m100) REVERT: D 334 SER cc_start: 0.6553 (p) cc_final: 0.6114 (p) REVERT: E 21 MET cc_start: 0.7238 (ppp) cc_final: 0.6385 (ttp) REVERT: A 832 PHE cc_start: 0.7017 (m-10) cc_final: 0.6740 (m-80) REVERT: B 446 ASN cc_start: 0.7797 (t0) cc_final: 0.7333 (t0) REVERT: B 558 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 29 LEU cc_start: 0.8857 (tp) cc_final: 0.8630 (tt) REVERT: C 203 MET cc_start: 0.7287 (mmt) cc_final: 0.7014 (mmt) REVERT: C 212 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7112 (mm-30) REVERT: C 256 ARG cc_start: 0.7305 (tpp-160) cc_final: 0.6684 (tpm170) REVERT: C 259 ILE cc_start: 0.8008 (mm) cc_final: 0.7327 (pt) REVERT: C 312 MET cc_start: 0.8181 (tpp) cc_final: 0.7938 (tmm) REVERT: C 321 ASP cc_start: 0.6901 (t0) cc_final: 0.6659 (t0) outliers start: 37 outliers final: 24 residues processed: 249 average time/residue: 0.1294 time to fit residues: 48.6590 Evaluate side-chains 243 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 60 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 71 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.087318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071197 restraints weight = 50136.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070967 restraints weight = 46480.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071619 restraints weight = 40328.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071904 restraints weight = 32649.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071951 restraints weight = 30973.342| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18004 Z= 0.112 Angle : 0.531 11.753 24467 Z= 0.276 Chirality : 0.042 0.231 2786 Planarity : 0.004 0.047 3061 Dihedral : 6.899 72.073 2761 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.96 % Allowed : 17.10 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.18), residues: 2209 helix: 1.62 (0.18), residues: 873 sheet: -0.88 (0.28), residues: 365 loop : -1.38 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 48 TYR 0.014 0.001 TYR B 751 PHE 0.039 0.001 PHE B 789 TRP 0.014 0.001 TRP A 299 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (17976) covalent geometry : angle 0.52623 / 0.27 (24401) SS BOND : bond 0.00261 / 0.16 ( 18) SS BOND : angle 1.60156 / 0.97 ( 36) hydrogen bonds : bond 0.04345 / 2.99 ( 732) hydrogen bonds : angle 3.94538 / 2.78 ( 2106) link_BETA1-4 : bond 0.00434 / 0.22 ( 3) link_BETA1-4 : angle 1.16200 / 0.71 ( 9) link_NAG-ASN : bond 0.00147 / 0.10 ( 7) link_NAG-ASN : angle 1.46714 / 0.96 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7489 (mpt180) REVERT: D 63 TRP cc_start: 0.7801 (m100) cc_final: 0.7452 (m100) REVERT: D 334 SER cc_start: 0.6480 (p) cc_final: 0.6059 (p) REVERT: E 21 MET cc_start: 0.7178 (ppp) cc_final: 0.6361 (ttp) REVERT: A 760 ILE cc_start: 0.8674 (mp) cc_final: 0.8229 (mm) REVERT: A 832 PHE cc_start: 0.6952 (m-10) cc_final: 0.6686 (m-80) REVERT: B 446 ASN cc_start: 0.7808 (t0) cc_final: 0.7362 (t0) REVERT: B 558 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 811 MET cc_start: 0.6737 (mmp) cc_final: 0.6396 (mmt) REVERT: B 854 PHE cc_start: 0.7280 (m-80) cc_final: 0.6771 (m-80) REVERT: C 29 LEU cc_start: 0.8852 (tp) cc_final: 0.8617 (tt) REVERT: C 203 MET cc_start: 0.7230 (mmt) cc_final: 0.6994 (mmt) REVERT: C 212 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6974 (mm-30) REVERT: C 256 ARG cc_start: 0.7342 (tpp-160) cc_final: 0.6758 (tpm170) REVERT: C 259 ILE cc_start: 0.7998 (mm) cc_final: 0.7334 (pt) REVERT: C 312 MET cc_start: 0.8155 (tpp) cc_final: 0.7951 (tmm) outliers start: 35 outliers final: 29 residues processed: 250 average time/residue: 0.1176 time to fit residues: 45.1488 Evaluate side-chains 254 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 37 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 155 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.087395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071297 restraints weight = 49913.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071092 restraints weight = 46495.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071768 restraints weight = 39988.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072268 restraints weight = 32513.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072392 restraints weight = 31548.950| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18004 Z= 0.117 Angle : 0.537 11.529 24467 Z= 0.280 Chirality : 0.042 0.231 2786 Planarity : 0.004 0.047 3061 Dihedral : 6.791 69.871 2761 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.96 % Allowed : 17.27 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2209 helix: 1.67 (0.18), residues: 871 sheet: -0.87 (0.28), residues: 365 loop : -1.37 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 873 TYR 0.025 0.001 TYR E 40 PHE 0.018 0.001 PHE C 220 TRP 0.013 0.001 TRP A 530 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17976) covalent geometry : angle 0.53259 / 0.28 (24401) SS BOND : bond 0.00221 / 0.15 ( 18) SS BOND : angle 1.56365 / 0.96 ( 36) hydrogen bonds : bond 0.04344 / 2.98 ( 732) hydrogen bonds : angle 3.92239 / 2.77 ( 2106) link_BETA1-4 : bond 0.00351 / 0.18 ( 3) link_BETA1-4 : angle 1.13877 / 0.69 ( 9) link_NAG-ASN : bond 0.00144 / 0.10 ( 7) link_NAG-ASN : angle 1.46467 / 0.96 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4418 Ramachandran restraints generated. 2209 Oldfield, 0 Emsley, 2209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7491 (mpt180) REVERT: D 63 TRP cc_start: 0.7797 (m100) cc_final: 0.7446 (m100) REVERT: D 334 SER cc_start: 0.6457 (p) cc_final: 0.6039 (p) REVERT: E 21 MET cc_start: 0.7182 (ppp) cc_final: 0.6358 (ttp) REVERT: A 760 ILE cc_start: 0.8670 (mp) cc_final: 0.8227 (mm) REVERT: A 832 PHE cc_start: 0.6996 (m-10) cc_final: 0.6738 (m-80) REVERT: B 446 ASN cc_start: 0.7798 (t0) cc_final: 0.7345 (t0) REVERT: B 558 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 733 PHE cc_start: 0.7277 (t80) cc_final: 0.7057 (t80) REVERT: B 811 MET cc_start: 0.6682 (mmp) cc_final: 0.6314 (mmt) REVERT: B 854 PHE cc_start: 0.7319 (m-80) cc_final: 0.6750 (m-80) REVERT: C 29 LEU cc_start: 0.8844 (tp) cc_final: 0.8613 (tt) REVERT: C 203 MET cc_start: 0.7182 (mmt) cc_final: 0.6965 (mmt) REVERT: C 212 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7015 (mm-30) REVERT: C 259 ILE cc_start: 0.8002 (mm) cc_final: 0.7330 (pt) REVERT: C 312 MET cc_start: 0.8161 (tpp) cc_final: 0.7955 (tmm) outliers start: 35 outliers final: 31 residues processed: 251 average time/residue: 0.1141 time to fit residues: 44.1206 Evaluate side-chains 258 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 463 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 145 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 93 optimal weight: 0.0060 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070999 restraints weight = 50159.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070700 restraints weight = 46604.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.071190 restraints weight = 41015.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071590 restraints weight = 33214.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071615 restraints weight = 31741.342| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18004 Z= 0.126 Angle : 0.538 11.302 24467 Z= 0.281 Chirality : 0.042 0.232 2786 Planarity : 0.004 0.047 3061 Dihedral : 6.695 66.360 2761 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.01 % Allowed : 17.38 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2209 helix: 1.64 (0.18), residues: 871 sheet: -0.89 (0.28), residues: 367 loop : -1.37 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 873 TYR 0.022 0.001 TYR E 40 PHE 0.014 0.001 PHE B 469 TRP 0.014 0.001 TRP A 530 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (17976) covalent geometry : angle 0.53340 / 0.28 (24401) SS BOND : bond 0.00250 / 0.16 ( 18) SS BOND : angle 1.47711 / 0.92 ( 36) hydrogen bonds : bond 0.04499 / 3.09 ( 732) hydrogen bonds : angle 3.93644 / 2.78 ( 2106) link_BETA1-4 : bond 0.00314 / 0.16 ( 3) link_BETA1-4 : angle 1.15075 / 0.70 ( 9) link_NAG-ASN : bond 0.00157 / 0.12 ( 7) link_NAG-ASN : angle 1.51997 / 1.01 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.81 seconds wall clock time: 43 minutes 48.98 seconds (2628.98 seconds total)