Starting phenix.real_space_refine on Sun Aug 24 06:18:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szg_40915/08_2025/8szg_40915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szg_40915/08_2025/8szg_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_40915/08_2025/8szg_40915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szg_40915/08_2025/8szg_40915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8szg_40915/08_2025/8szg_40915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szg_40915/08_2025/8szg_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 159 Unusual residues: {' CA': 3, 'NAG': 2, 'PCW': 1, 'PO4': 1, 'SPM': 2, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1208 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} 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: 3.28, 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: 1.33 Conformation dependent library (CDL) restraints added in 580.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.36 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: 2.53 Time building geometry restraints manager: 1.65 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: 9.830 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: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.960 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:1.350 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: 0.7514 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 aren 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 covalent geometry : bond 0.00632 (17976) covalent geometry : angle 0.85083 (24401) SS BOND : bond 0.00241 ( 18) SS BOND : angle 1.60138 ( 36) hydrogen bonds : bond 0.19316 ( 732) hydrogen bonds : angle 6.38958 ( 2106) link_BETA1-4 : bond 0.00536 ( 3) link_BETA1-4 : angle 1.21680 ( 9) link_NAG-ASN : bond 0.00146 ( 7) link_NAG-ASN : angle 1.50539 ( 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 : 0.491 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: 0.1172 time to fit residues: 53.0710 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 : 0.433 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.087965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071895 restraints weight = 49713.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071951 restraints weight = 42772.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072611 restraints weight = 37174.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072960 restraints weight = 29782.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073149 restraints weight = 29246.300| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18004 Z= 0.138 Angle : 0.568 9.504 24467 Z= 0.301 Chirality : 0.043 0.255 2786 Planarity : 0.004 0.050 3061 Dihedral : 8.738 84.042 2762 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.17 % Allowed : 8.50 % Favored : 90.33 % 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 aren 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 0.005 0.000 ARG E 13 TYR 0.016 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 covalent geometry : bond 0.00301 (17976) covalent geometry : angle 0.56087 (24401) SS BOND : bond 0.00288 ( 18) SS BOND : angle 2.19869 ( 36) hydrogen bonds : bond 0.05962 ( 732) hydrogen bonds : angle 4.62355 ( 2106) link_BETA1-4 : bond 0.00279 ( 3) link_BETA1-4 : angle 1.09373 ( 9) link_NAG-ASN : bond 0.00190 ( 7) link_NAG-ASN : angle 1.36348 ( 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 : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8671 (mppt) cc_final: 0.8411 (mmtm) REVERT: D 63 TRP cc_start: 0.7689 (m100) cc_final: 0.7314 (m100) REVERT: E 21 MET cc_start: 0.7325 (ppp) cc_final: 0.6148 (ttp) REVERT: A 760 ILE cc_start: 0.8646 (mt) cc_final: 0.8303 (mm) REVERT: A 790 PHE cc_start: 0.8061 (m-10) cc_final: 0.7690 (m-80) REVERT: A 829 TYR cc_start: 0.7995 (p90) cc_final: 0.7624 (p90) REVERT: A 832 PHE cc_start: 0.6990 (m-10) cc_final: 0.6703 (m-80) REVERT: B 446 ASN cc_start: 0.7769 (t0) cc_final: 0.7542 (t0) REVERT: B 558 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 738 ILE cc_start: 0.7372 (tp) cc_final: 0.7068 (tt) REVERT: B 848 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7738 (tt) REVERT: B 852 ILE cc_start: 0.8500 (mt) cc_final: 0.8279 (mm) REVERT: C 29 LEU cc_start: 0.8815 (tp) cc_final: 0.8557 (tt) REVERT: C 259 ILE cc_start: 0.8138 (mm) cc_final: 0.7486 (pt) REVERT: C 321 ASP cc_start: 0.7058 (t0) cc_final: 0.6804 (t0) outliers start: 21 outliers final: 10 residues processed: 261 average time/residue: 0.1172 time to fit residues: 46.2471 Evaluate side-chains 244 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 233 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 162 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 109 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 700 ASN B 800 ASN ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.087750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071387 restraints weight = 49982.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071811 restraints weight = 41598.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072344 restraints weight = 34230.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072444 restraints weight = 28787.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072619 restraints weight = 25489.361| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18004 Z= 0.135 Angle : 0.530 9.932 24467 Z= 0.279 Chirality : 0.042 0.231 2786 Planarity : 0.004 0.044 3061 Dihedral : 8.250 81.472 2761 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.40 % Allowed : 11.07 % Favored : 87.53 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2209 helix: 1.50 (0.18), residues: 880 sheet: -0.71 (0.28), residues: 365 loop : -1.30 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 13 TYR 0.015 0.001 TYR B 751 PHE 0.017 0.001 PHE A 814 TRP 0.016 0.001 TRP B 818 HIS 0.006 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00307 (17976) covalent geometry : angle 0.52615 (24401) SS BOND : bond 0.00740 ( 18) SS BOND : angle 1.40353 ( 36) hydrogen bonds : bond 0.05156 ( 732) hydrogen bonds : angle 4.26008 ( 2106) link_BETA1-4 : bond 0.00349 ( 3) link_BETA1-4 : angle 1.19553 ( 9) link_NAG-ASN : bond 0.00160 ( 7) link_NAG-ASN : angle 1.45586 ( 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 268 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 243 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 LYS cc_start: 0.8681 (mppt) cc_final: 0.8476 (mmtm) REVERT: D 63 TRP cc_start: 0.7721 (m100) cc_final: 0.7332 (m100) REVERT: A 760 ILE cc_start: 0.8615 (mt) cc_final: 0.8306 (mm) REVERT: A 790 PHE cc_start: 0.8072 (m-10) cc_final: 0.7697 (m-80) REVERT: A 829 TYR cc_start: 0.7990 (p90) cc_final: 0.7720 (p90) REVERT: A 832 PHE cc_start: 0.7038 (m-10) cc_final: 0.6789 (m-80) REVERT: B 446 ASN cc_start: 0.7758 (t0) cc_final: 0.7405 (t0) REVERT: B 558 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 738 ILE cc_start: 0.7420 (tp) cc_final: 0.7144 (tt) REVERT: C 29 LEU cc_start: 0.8810 (tp) cc_final: 0.8549 (tt) REVERT: C 252 LYS cc_start: 0.7307 (mtpp) cc_final: 0.6698 (mtmm) REVERT: C 259 ILE cc_start: 0.8151 (mm) cc_final: 0.7477 (pt) REVERT: C 312 MET cc_start: 0.8119 (tpp) cc_final: 0.7838 (tmm) REVERT: C 321 ASP cc_start: 0.7057 (t0) cc_final: 0.6840 (t0) outliers start: 25 outliers final: 15 residues processed: 252 average time/residue: 0.1246 time to fit residues: 47.1121 Evaluate side-chains 245 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 727 LEU Chi-restraints excluded: chain B residue 740 VAL 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: 1.9990 chunk 32 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 86 optimal weight: 0.0170 chunk 107 optimal weight: 6.9990 chunk 151 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** 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 = 0.3537 r_free = 0.3537 target = 0.087030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070835 restraints weight = 50160.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070894 restraints weight = 44100.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071545 restraints weight = 37278.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.071715 restraints weight = 30324.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071917 restraints weight = 26966.191| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18004 Z= 0.159 Angle : 0.544 12.313 24467 Z= 0.286 Chirality : 0.043 0.232 2786 Planarity : 0.004 0.045 3061 Dihedral : 7.887 77.554 2761 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.73 % Allowed : 12.35 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.18), residues: 2209 helix: 1.45 (0.18), residues: 885 sheet: -0.79 (0.28), residues: 365 loop : -1.33 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 873 TYR 0.015 0.001 TYR E 40 PHE 0.020 0.001 PHE A 625 TRP 0.016 0.001 TRP C 263 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00379 (17976) covalent geometry : angle 0.53986 (24401) SS BOND : bond 0.00290 ( 18) SS BOND : angle 1.40076 ( 36) hydrogen bonds : bond 0.05279 ( 732) hydrogen bonds : angle 4.18380 ( 2106) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.21198 ( 9) link_NAG-ASN : bond 0.00221 ( 7) link_NAG-ASN : angle 1.61522 ( 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 270 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7757 (m100) cc_final: 0.7389 (m100) REVERT: D 234 PHE cc_start: 0.5366 (t80) cc_final: 0.5088 (t80) REVERT: A 760 ILE cc_start: 0.8651 (mt) cc_final: 0.8285 (mm) REVERT: A 790 PHE cc_start: 0.8113 (m-10) cc_final: 0.7776 (m-10) REVERT: A 829 TYR cc_start: 0.7988 (p90) cc_final: 0.7738 (p90) REVERT: A 832 PHE cc_start: 0.7056 (m-10) cc_final: 0.6772 (m-80) REVERT: B 446 ASN cc_start: 0.7771 (t0) cc_final: 0.7372 (t0) REVERT: B 558 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 738 ILE cc_start: 0.7504 (tp) cc_final: 0.7264 (tp) REVERT: C 27 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7298 (ptp-170) REVERT: C 29 LEU cc_start: 0.8809 (tp) cc_final: 0.8552 (tt) REVERT: C 252 LYS cc_start: 0.7514 (mtpp) cc_final: 0.7121 (mtpp) REVERT: C 259 ILE cc_start: 0.8161 (mm) cc_final: 0.7442 (pt) outliers start: 31 outliers final: 26 residues processed: 253 average time/residue: 0.1247 time to fit residues: 47.5011 Evaluate side-chains 250 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 358 CYS 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 732 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain B residue 343 VAL 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 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 815 PHE 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 344 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 14 optimal weight: 0.9980 chunk 171 optimal weight: 0.1980 chunk 181 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS A 253 GLN B 359 HIS ** B 471 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 = 0.3558 r_free = 0.3558 target = 0.087985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071745 restraints weight = 49758.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072010 restraints weight = 42574.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072567 restraints weight = 38591.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072809 restraints weight = 29998.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072868 restraints weight = 29413.313| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18004 Z= 0.116 Angle : 0.508 11.541 24467 Z= 0.265 Chirality : 0.042 0.229 2786 Planarity : 0.004 0.045 3061 Dihedral : 7.373 77.800 2761 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.62 % Allowed : 13.36 % Favored : 85.02 % 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 aren not related in a simple way. whole: -0.09 (0.18), residues: 2209 helix: 1.57 (0.18), residues: 882 sheet: -0.78 (0.28), residues: 365 loop : -1.32 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.012 0.001 TYR B 751 PHE 0.018 0.001 PHE B 789 TRP 0.013 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00260 (17976) covalent geometry : angle 0.50305 (24401) SS BOND : bond 0.00273 ( 18) SS BOND : angle 1.42476 ( 36) hydrogen bonds : bond 0.04532 ( 732) hydrogen bonds : angle 4.03158 ( 2106) link_BETA1-4 : bond 0.00313 ( 3) link_BETA1-4 : angle 1.09460 ( 9) link_NAG-ASN : bond 0.00154 ( 7) link_NAG-ASN : angle 1.44186 ( 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 266 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7747 (m100) cc_final: 0.7377 (m100) REVERT: D 234 PHE cc_start: 0.5361 (t80) cc_final: 0.5092 (t80) REVERT: A 760 ILE cc_start: 0.8606 (mt) cc_final: 0.8303 (mm) REVERT: A 790 PHE cc_start: 0.8124 (m-10) cc_final: 0.7741 (m-80) REVERT: A 829 TYR cc_start: 0.7946 (p90) cc_final: 0.7727 (p90) REVERT: A 832 PHE cc_start: 0.7006 (m-10) cc_final: 0.6737 (m-80) REVERT: B 446 ASN cc_start: 0.7729 (t0) cc_final: 0.7328 (t0) REVERT: B 558 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 738 ILE cc_start: 0.7510 (tp) cc_final: 0.7296 (tt) REVERT: C 29 LEU cc_start: 0.8802 (tp) cc_final: 0.8542 (tt) REVERT: C 212 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6831 (mm-30) REVERT: C 259 ILE cc_start: 0.8099 (mm) cc_final: 0.7422 (pt) REVERT: C 312 MET cc_start: 0.8114 (tpp) cc_final: 0.7795 (tmm) REVERT: C 321 ASP cc_start: 0.6812 (t0) cc_final: 0.6602 (t0) outliers start: 29 outliers final: 17 residues processed: 249 average time/residue: 0.1223 time to fit residues: 46.5023 Evaluate side-chains 239 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 358 CYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 763 ILE 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 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 766 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 212 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 164 optimal weight: 0.1980 chunk 176 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 25 optimal weight: 0.0870 chunk 140 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN B 359 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070906 restraints weight = 49849.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.070901 restraints weight = 42848.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071441 restraints weight = 39879.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071786 restraints weight = 30976.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071890 restraints weight = 28065.678| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18004 Z= 0.130 Angle : 0.524 10.743 24467 Z= 0.275 Chirality : 0.042 0.231 2786 Planarity : 0.004 0.045 3061 Dihedral : 7.173 77.336 2761 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.18 % Allowed : 13.42 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.18), residues: 2209 helix: 1.64 (0.18), residues: 873 sheet: -0.79 (0.28), residues: 365 loop : -1.32 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.013 0.001 TYR B 744 PHE 0.024 0.001 PHE B 789 TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00303 (17976) covalent geometry : angle 0.51910 (24401) SS BOND : bond 0.00226 ( 18) SS BOND : angle 1.43261 ( 36) hydrogen bonds : bond 0.04670 ( 732) hydrogen bonds : angle 4.01434 ( 2106) link_BETA1-4 : bond 0.00303 ( 3) link_BETA1-4 : angle 1.17670 ( 9) link_NAG-ASN : bond 0.00166 ( 7) link_NAG-ASN : angle 1.49068 ( 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 272 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7766 (m100) cc_final: 0.7398 (m100) REVERT: D 234 PHE cc_start: 0.5361 (t80) cc_final: 0.5112 (t80) REVERT: D 334 SER cc_start: 0.6528 (p) cc_final: 0.6106 (p) REVERT: E 21 MET cc_start: 0.7207 (ppp) cc_final: 0.6227 (ttp) REVERT: A 760 ILE cc_start: 0.8628 (mt) cc_final: 0.8328 (mm) REVERT: A 790 PHE cc_start: 0.8159 (m-10) cc_final: 0.7807 (m-80) REVERT: A 832 PHE cc_start: 0.7014 (m-10) cc_final: 0.6748 (m-80) REVERT: B 446 ASN cc_start: 0.7788 (t0) cc_final: 0.7370 (t0) REVERT: B 558 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 811 MET cc_start: 0.6683 (mmp) cc_final: 0.6441 (mmt) REVERT: C 29 LEU cc_start: 0.8826 (tp) cc_final: 0.8564 (tt) REVERT: C 212 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6902 (mm-30) REVERT: C 259 ILE cc_start: 0.8043 (mm) cc_final: 0.7371 (pt) REVERT: C 312 MET cc_start: 0.8141 (tpp) cc_final: 0.7788 (tmm) REVERT: C 321 ASP cc_start: 0.6685 (t0) cc_final: 0.6456 (t0) REVERT: C 322 LYS cc_start: 0.5962 (pttp) cc_final: 0.5699 (pttp) outliers start: 39 outliers final: 28 residues processed: 254 average time/residue: 0.1144 time to fit residues: 44.0510 Evaluate side-chains 249 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 358 CYS 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 732 THR 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 343 VAL 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 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 740 VAL Chi-restraints excluded: chain B residue 766 HIS 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 218 HIS 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: 0.9980 chunk 19 optimal weight: 5.9990 chunk 200 optimal weight: 0.4980 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 0.3980 chunk 205 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.087560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071267 restraints weight = 49863.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071320 restraints weight = 42521.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072015 restraints weight = 36382.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072342 restraints weight = 29760.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072493 restraints weight = 28589.752| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18004 Z= 0.116 Angle : 0.508 11.621 24467 Z= 0.265 Chirality : 0.042 0.230 2786 Planarity : 0.004 0.045 3061 Dihedral : 6.982 76.529 2761 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.90 % Allowed : 14.25 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.18), residues: 2209 helix: 1.67 (0.18), residues: 873 sheet: -0.79 (0.28), residues: 365 loop : -1.29 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 866 TYR 0.013 0.001 TYR B 751 PHE 0.029 0.001 PHE B 789 TRP 0.013 0.001 TRP A 530 HIS 0.021 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00263 (17976) covalent geometry : angle 0.50361 (24401) SS BOND : bond 0.00206 ( 18) SS BOND : angle 1.38600 ( 36) hydrogen bonds : bond 0.04450 ( 732) hydrogen bonds : angle 3.94396 ( 2106) link_BETA1-4 : bond 0.00318 ( 3) link_BETA1-4 : angle 1.12261 ( 9) link_NAG-ASN : bond 0.00145 ( 7) link_NAG-ASN : angle 1.44399 ( 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 264 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7784 (m100) cc_final: 0.7426 (m100) REVERT: D 334 SER cc_start: 0.6488 (p) cc_final: 0.6072 (p) REVERT: A 760 ILE cc_start: 0.8635 (mt) cc_final: 0.8349 (mm) REVERT: A 790 PHE cc_start: 0.8156 (m-10) cc_final: 0.7795 (m-80) REVERT: A 832 PHE cc_start: 0.6950 (m-10) cc_final: 0.6685 (m-80) REVERT: B 446 ASN cc_start: 0.7780 (t0) cc_final: 0.7351 (t0) REVERT: B 558 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 811 MET cc_start: 0.6670 (mmp) cc_final: 0.6460 (mmt) REVERT: C 29 LEU cc_start: 0.8828 (tp) cc_final: 0.8564 (tt) REVERT: C 259 ILE cc_start: 0.8035 (mm) cc_final: 0.7373 (pt) REVERT: C 312 MET cc_start: 0.8133 (tpp) cc_final: 0.7784 (tmm) REVERT: C 321 ASP cc_start: 0.6739 (t0) cc_final: 0.6448 (t0) outliers start: 34 outliers final: 27 residues processed: 249 average time/residue: 0.1183 time to fit residues: 44.5134 Evaluate side-chains 251 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 358 CYS Chi-restraints excluded: chain A residue 429 HIS 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 763 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL 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 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 740 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 766 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 138 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 56 optimal weight: 0.0570 chunk 134 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071776 restraints weight = 49749.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072432 restraints weight = 40083.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072955 restraints weight = 31339.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073103 restraints weight = 25807.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073203 restraints weight = 24025.959| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18004 Z= 0.106 Angle : 0.505 10.677 24467 Z= 0.264 Chirality : 0.041 0.229 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.716 74.897 2761 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.01 % Allowed : 14.31 % Favored : 83.68 % 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 aren not related in a simple way. whole: 0.05 (0.18), residues: 2209 helix: 1.76 (0.18), residues: 871 sheet: -0.78 (0.28), residues: 371 loop : -1.27 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.013 0.001 TYR B 751 PHE 0.013 0.001 PHE B 469 TRP 0.012 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00238 (17976) covalent geometry : angle 0.50150 (24401) SS BOND : bond 0.00187 ( 18) SS BOND : angle 1.29532 ( 36) hydrogen bonds : bond 0.04153 ( 732) hydrogen bonds : angle 3.86773 ( 2106) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 1.08811 ( 9) link_NAG-ASN : bond 0.00142 ( 7) link_NAG-ASN : angle 1.37075 ( 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: 36 poor density : 228 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7768 (m100) cc_final: 0.7418 (m100) REVERT: D 334 SER cc_start: 0.6419 (p) cc_final: 0.6001 (p) REVERT: E 21 MET cc_start: 0.7272 (ppp) cc_final: 0.6388 (ttp) REVERT: A 719 TRP cc_start: 0.6817 (t60) cc_final: 0.6204 (t-100) REVERT: A 760 ILE cc_start: 0.8639 (mt) cc_final: 0.8349 (mm) REVERT: A 790 PHE cc_start: 0.8154 (m-10) cc_final: 0.7791 (m-80) REVERT: A 832 PHE cc_start: 0.6906 (m-10) cc_final: 0.6656 (m-80) REVERT: B 446 ASN cc_start: 0.7801 (t0) cc_final: 0.7378 (t0) REVERT: B 558 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 811 MET cc_start: 0.6662 (mmp) cc_final: 0.6354 (mmt) REVERT: C 29 LEU cc_start: 0.8849 (tp) cc_final: 0.8625 (tt) REVERT: C 212 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 259 ILE cc_start: 0.8019 (mm) cc_final: 0.7355 (pt) REVERT: C 321 ASP cc_start: 0.6606 (t0) cc_final: 0.6257 (t0) outliers start: 36 outliers final: 24 residues processed: 247 average time/residue: 0.1159 time to fit residues: 44.0674 Evaluate side-chains 248 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 A residue 358 CYS Chi-restraints excluded: chain A residue 429 HIS 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 763 ILE 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 486 VAL Chi-restraints excluded: chain B residue 627 THR 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 740 VAL Chi-restraints excluded: chain B residue 743 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 191 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 219 optimal weight: 0.0980 chunk 35 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3576 r_free = 0.3576 target = 0.088833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072251 restraints weight = 49885.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073025 restraints weight = 40310.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073543 restraints weight = 31424.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073772 restraints weight = 25255.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073884 restraints weight = 23552.755| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18004 Z= 0.103 Angle : 0.505 10.332 24467 Z= 0.263 Chirality : 0.041 0.230 2786 Planarity : 0.003 0.046 3061 Dihedral : 6.448 72.262 2761 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.73 % Allowed : 15.32 % Favored : 82.95 % 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 aren not related in a simple way. whole: 0.11 (0.18), residues: 2209 helix: 1.81 (0.18), residues: 871 sheet: -0.77 (0.28), residues: 366 loop : -1.22 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.012 0.001 TYR B 751 PHE 0.033 0.001 PHE B 789 TRP 0.011 0.001 TRP A 530 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00229 (17976) covalent geometry : angle 0.50202 (24401) SS BOND : bond 0.00177 ( 18) SS BOND : angle 1.18360 ( 36) hydrogen bonds : bond 0.03931 ( 732) hydrogen bonds : angle 3.79782 ( 2106) link_BETA1-4 : bond 0.00355 ( 3) link_BETA1-4 : angle 1.06915 ( 9) link_NAG-ASN : bond 0.00142 ( 7) link_NAG-ASN : angle 1.33162 ( 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 265 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7724 (m100) cc_final: 0.7315 (m100) REVERT: D 139 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6886 (mt) REVERT: D 334 SER cc_start: 0.6376 (p) cc_final: 0.5958 (p) REVERT: E 21 MET cc_start: 0.7221 (ppp) cc_final: 0.6418 (ttp) REVERT: A 719 TRP cc_start: 0.6798 (t60) cc_final: 0.6180 (t-100) REVERT: A 745 THR cc_start: 0.8341 (t) cc_final: 0.8019 (t) REVERT: A 760 ILE cc_start: 0.8630 (mt) cc_final: 0.8342 (mm) REVERT: A 790 PHE cc_start: 0.8156 (m-10) cc_final: 0.7779 (m-80) REVERT: A 832 PHE cc_start: 0.6864 (m-10) cc_final: 0.6616 (m-80) REVERT: B 446 ASN cc_start: 0.7812 (t0) cc_final: 0.7305 (t0) REVERT: B 558 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 733 PHE cc_start: 0.7170 (t80) cc_final: 0.6928 (t80) REVERT: C 29 LEU cc_start: 0.8853 (tp) cc_final: 0.8622 (tt) REVERT: C 259 ILE cc_start: 0.7994 (mm) cc_final: 0.7342 (pt) REVERT: C 321 ASP cc_start: 0.6583 (t0) cc_final: 0.6191 (t0) outliers start: 31 outliers final: 24 residues processed: 250 average time/residue: 0.1208 time to fit residues: 45.9426 Evaluate side-chains 255 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 A residue 358 CYS 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 744 TYR Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL 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 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 743 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 191 GLU Chi-restraints excluded: chain C residue 218 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 37 optimal weight: 0.0770 chunk 181 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS C 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072188 restraints weight = 49667.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072429 restraints weight = 44709.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072932 restraints weight = 39532.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073096 restraints weight = 33444.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073285 restraints weight = 28858.547| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18004 Z= 0.120 Angle : 0.529 10.194 24467 Z= 0.275 Chirality : 0.042 0.239 2786 Planarity : 0.004 0.045 3061 Dihedral : 6.439 71.354 2761 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.84 % Allowed : 15.48 % Favored : 82.67 % 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 aren not related in a simple way. whole: 0.08 (0.18), residues: 2209 helix: 1.77 (0.18), residues: 872 sheet: -0.77 (0.28), residues: 366 loop : -1.23 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 873 TYR 0.024 0.001 TYR E 40 PHE 0.041 0.001 PHE A 853 TRP 0.017 0.001 TRP D 169 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00279 (17976) covalent geometry : angle 0.52616 (24401) SS BOND : bond 0.00177 ( 18) SS BOND : angle 1.21953 ( 36) hydrogen bonds : bond 0.04171 ( 732) hydrogen bonds : angle 3.83119 ( 2106) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 1.10195 ( 9) link_NAG-ASN : bond 0.00133 ( 7) link_NAG-ASN : angle 1.37724 ( 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 262 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 TRP cc_start: 0.7778 (m100) cc_final: 0.7398 (m100) REVERT: D 139 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6900 (mt) REVERT: D 334 SER cc_start: 0.6405 (p) cc_final: 0.5977 (p) REVERT: E 13 ARG cc_start: 0.6481 (tpm170) cc_final: 0.6148 (tpt90) REVERT: E 21 MET cc_start: 0.7212 (ppp) cc_final: 0.6392 (ttp) REVERT: A 719 TRP cc_start: 0.6830 (t60) cc_final: 0.6226 (t-100) REVERT: A 745 THR cc_start: 0.8298 (t) cc_final: 0.7973 (t) REVERT: A 760 ILE cc_start: 0.8652 (mt) cc_final: 0.8363 (mm) REVERT: A 790 PHE cc_start: 0.8165 (m-10) cc_final: 0.7778 (m-80) REVERT: A 832 PHE cc_start: 0.6882 (m-10) cc_final: 0.6645 (m-80) REVERT: B 446 ASN cc_start: 0.7798 (t0) cc_final: 0.7271 (t0) REVERT: B 558 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 733 PHE cc_start: 0.7209 (t80) cc_final: 0.6959 (t80) REVERT: C 29 LEU cc_start: 0.8841 (tp) cc_final: 0.8614 (tt) REVERT: C 259 ILE cc_start: 0.7997 (mm) cc_final: 0.7353 (pt) REVERT: C 306 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.5655 (ptp-170) REVERT: C 321 ASP cc_start: 0.6588 (t0) cc_final: 0.6185 (t0) outliers start: 33 outliers final: 26 residues processed: 246 average time/residue: 0.1249 time to fit residues: 46.7884 Evaluate side-chains 256 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 732 THR Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 343 VAL 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 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 766 HIS 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 218 HIS Chi-restraints excluded: chain C residue 306 ARG 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: 0.0050 chunk 176 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 150 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3578 r_free = 0.3578 target = 0.088879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072709 restraints weight = 49931.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072739 restraints weight = 43153.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073322 restraints weight = 37920.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073921 restraints weight = 29935.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074009 restraints weight = 28681.861| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18004 Z= 0.106 Angle : 0.517 9.944 24467 Z= 0.268 Chirality : 0.042 0.229 2786 Planarity : 0.003 0.045 3061 Dihedral : 6.173 68.797 2761 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.68 % Allowed : 15.76 % Favored : 82.56 % 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 aren not related in a simple way. whole: 0.12 (0.18), residues: 2209 helix: 1.77 (0.18), residues: 878 sheet: -0.74 (0.28), residues: 366 loop : -1.19 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 638 TYR 0.022 0.001 TYR E 40 PHE 0.016 0.001 PHE B 619 TRP 0.014 0.001 TRP D 169 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00237 (17976) covalent geometry : angle 0.51359 (24401) SS BOND : bond 0.00174 ( 18) SS BOND : angle 1.14186 ( 36) hydrogen bonds : bond 0.03942 ( 732) hydrogen bonds : angle 3.79073 ( 2106) link_BETA1-4 : bond 0.00355 ( 3) link_BETA1-4 : angle 1.06990 ( 9) link_NAG-ASN : bond 0.00137 ( 7) link_NAG-ASN : angle 1.33332 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.58 seconds wall clock time: 43 minutes 5.02 seconds (2585.02 seconds total)