Starting phenix.real_space_refine on Wed Jul 30 20:32:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpg_37716/07_2025/8wpg_37716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpg_37716/07_2025/8wpg_37716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpg_37716/07_2025/8wpg_37716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpg_37716/07_2025/8wpg_37716.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpg_37716/07_2025/8wpg_37716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpg_37716/07_2025/8wpg_37716.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.085 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 4 9.91 5 P 2 5.49 5 S 62 5.16 5 C 8023 2.51 5 N 2030 2.21 5 O 2316 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 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12443 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 6096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6096 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 179 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6069 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 200 Chain: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "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: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CA': 3, 'PO4': 1, 'YP4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'PO4': 1, 'YP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.14, per 1000 atoms: 0.65 Number of scatterers: 12443 At special positions: 0 Unit cell: (97.37, 89.88, 185.11, 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 4 19.99 S 62 16.00 P 2 15.00 F 6 9.00 O 2316 8.00 N 2030 7.00 C 8023 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 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=2.21 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 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 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 468 " " NAG C 1 " - " ASN B 541 " " NAG D 1 " - " ASN B 488 " " NAG E 1 " - " ASN A 488 " " NAG F 1 " - " ASN A 541 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3028 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 49.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.631A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.512A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.574A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 612 through 637 Processing helix chain 'B' and resid 649 through 665 removed outlier: 3.629A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.660A pdb=" N CYS B 677 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 678' Processing helix chain 'B' and resid 679 through 699 removed outlier: 3.771A pdb=" N VAL B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.796A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 791 Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.766A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 828 Processing helix chain 'B' and resid 830 through 833 Processing helix chain 'B' and resid 834 through 853 removed outlier: 4.502A pdb=" N LEU B 842 " --> pdb=" O VAL B 838 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.660A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.510A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.534A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.403A pdb=" N SER A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) 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 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.809A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 Processing helix chain 'A' and resid 647 through 665 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 679 removed outlier: 3.627A pdb=" N LEU A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 700 removed outlier: 3.743A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.714A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.772A pdb=" N LEU A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE A 790 " --> pdb=" O ILE A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 803 through 820 removed outlier: 3.763A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 831 through 861 removed outlier: 3.915A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.169A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.855A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.322A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AA6, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'B' and resid 602 through 604 Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.320A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 33 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N VAL A 142 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY A 35 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.847A 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: 7.646A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 removed outlier: 5.973A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1665 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: 4.08 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3950 1.34 - 1.46: 3169 1.46 - 1.58: 5547 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 12740 Sorted by residual: bond pdb=" O4 PO4 B 908 " pdb=" P PO4 B 908 " ideal model delta sigma weight residual 1.568 1.503 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O2 PO4 B 908 " pdb=" P PO4 B 908 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" O3 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" O2 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.567 1.505 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" O3 PO4 B 908 " pdb=" P PO4 B 908 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 12735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 17171 2.59 - 5.18: 155 5.18 - 7.76: 16 7.76 - 10.35: 3 10.35 - 12.94: 1 Bond angle restraints: 17346 Sorted by residual: angle pdb=" N ILE A 819 " pdb=" CA ILE A 819 " pdb=" C ILE A 819 " ideal model delta sigma weight residual 112.96 108.16 4.80 1.00e+00 1.00e+00 2.30e+01 angle pdb=" N ASN B 867 " pdb=" CA ASN B 867 " pdb=" C ASN B 867 " ideal model delta sigma weight residual 108.07 114.46 -6.39 1.38e+00 5.25e-01 2.14e+01 angle pdb=" CA PRO A 682 " pdb=" N PRO A 682 " pdb=" CD PRO A 682 " ideal model delta sigma weight residual 112.00 106.51 5.49 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA LEU A 783 " pdb=" CB LEU A 783 " pdb=" CG LEU A 783 " ideal model delta sigma weight residual 116.30 129.24 -12.94 3.50e+00 8.16e-02 1.37e+01 angle pdb=" C PRO B 864 " pdb=" N SER B 865 " pdb=" CA SER B 865 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 17341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6598 17.66 - 35.32: 761 35.32 - 52.98: 224 52.98 - 70.64: 44 70.64 - 88.30: 16 Dihedral angle restraints: 7643 sinusoidal: 2967 harmonic: 4676 Sorted by residual: 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 93.00 179.02 -86.02 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual -86.00 -139.09 53.09 1 1.00e+01 1.00e-02 3.84e+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 93.00 143.59 -50.59 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 7640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1616 0.054 - 0.109: 315 0.109 - 0.163: 57 0.163 - 0.217: 1 0.217 - 0.272: 2 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CB ILE B 816 " pdb=" CA ILE B 816 " pdb=" CG1 ILE B 816 " pdb=" CG2 ILE B 816 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA YP4 A 906 " pdb=" N YP4 A 906 " pdb=" CB YP4 A 906 " pdb=" C1 YP4 A 906 " both_signs ideal model delta sigma weight residual False -2.41 -2.64 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA YP4 B 909 " pdb=" N YP4 B 909 " pdb=" CB YP4 B 909 " pdb=" C1 YP4 B 909 " both_signs ideal model delta sigma weight residual False -2.41 -2.61 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1988 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 135 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 136 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 681 " -0.051 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO A 682 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 682 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 682 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 671 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 672 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 672 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 672 " -0.031 5.00e-02 4.00e+02 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 424 2.71 - 3.26: 12360 3.26 - 3.81: 21037 3.81 - 4.35: 26208 4.35 - 4.90: 43487 Nonbonded interactions: 103516 Sorted by model distance: nonbonded pdb=" O TRP A 818 " pdb=" F1 YP4 A 906 " model vdw 2.163 2.990 nonbonded pdb=" O TRP B 818 " pdb=" F1 YP4 B 909 " model vdw 2.170 2.990 nonbonded pdb=" O ALA B 548 " pdb=" OG SER B 574 " model vdw 2.184 3.040 nonbonded pdb=" NH1 ARG B 69 " pdb=" O PRO B 407 " model vdw 2.187 3.120 nonbonded pdb=" O VAL B 314 " pdb=" OG1 THR B 317 " model vdw 2.189 3.040 ... (remaining 103511 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 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 359 or (resid 360 and (name N or n \ ame CA or name C or name O or name CB )) or resid 361 through 397 or (resid 398 \ and (name N or name CA or name C or name O or name CB )) or resid 399 through 44 \ 0 or (resid 441 and (name N or name CA or name C or name O or name CB )) or resi \ d 442 through 499 or (resid 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 515 or (resid 516 and (name N or name CA or name C \ or name O or name CB )) or resid 517 through 591 or (resid 592 through 593 and \ (name N or name CA or name C or name O or name CB )) or resid 594 through 603 or \ (resid 604 and (name N or name CA or name C or name O or name CB )) or resid 60 \ 5 through 613 or (resid 614 through 615 and (name N or name CA or name C or name \ O or name CB )) or resid 616 through 630 or (resid 631 and (name N or name CA o \ r name C or name O or name CB )) or resid 632 through 634 or (resid 635 through \ 636 and (name N or name CA or name C or name O or name CB )) or resid 637 throug \ h 638 or (resid 639 and (name N or name CA or name C or name O or name CB )) or \ resid 640 through 643 or (resid 644 through 646 and (name N or name CA or name C \ or name O or name CB )) or resid 647 through 660 or (resid 661 and (name N or n \ ame CA or name C or name O or name CB )) or resid 662 through 673 or (resid 674 \ and (name N or name CA or name C or name O or name CB )) or resid 675 or (resid \ 676 and (name N or name CA or name C or name O or name CB )) or resid 677 throug \ h 679 or (resid 680 through 681 and (name N or name CA or name C or name O or na \ me CB )) or resid 682 through 702 or resid 722 through 725 or (resid 726 and (na \ me N or name CA or name C or name O or name CB )) or resid 727 through 739 or (r \ esid 740 through 741 and (name N or name CA or name C or name O or name CB )) or \ resid 742 through 744 or (resid 745 through 746 and (name N or name CA or name \ C or name O or name CB )) or resid 747 through 785 or (resid 786 through 789 and \ (name N or name CA or name C or name O or name CB )) or resid 790 through 800 o \ r (resid 801 through 806 and (name N or name CA or name C or name O or name CB ) \ ) or resid 807 through 812 or (resid 813 and (name N or name CA or name C or nam \ e O or name CB )) or resid 814 through 826 or (resid 827 and (name N or name CA \ or name C or name O or name CB )) or resid 828 through 837 or (resid 838 and (na \ me N or name CA or name C or name O or name CB )) or resid 839 through 850 or (r \ esid 851 and (name N or name CA or name C or name O or name CB )) or resid 852 t \ hrough 854 or (resid 855 and (name N or name CA or name C or name O or name CB ) \ ) or resid 856 or (resid 857 and (name N or name CA or name C or name O or name \ CB )) or resid 858 through 860 or (resid 861 through 863 and (name N or name CA \ or name C or name O or name CB )) or resid 864 through 872 or resid 901 through \ 903 or resid 904)) selection = (chain 'B' and (resid 20 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 or (resid 50 and (name N or name CA or nam \ e C or name O or name CB )) or resid 51 through 127 or (resid 131 through 135 an \ d (name N or name CA or name C or name O or name CB )) or resid 136 through 222 \ or (resid 223 and (name N or name CA or name C or name O or name CB )) or resid \ 224 through 261 or (resid 262 and (name N or name CA or name C or name O or name \ CB )) or resid 263 through 362 or resid 392 through 451 or (resid 452 through 4 \ 53 and (name N or name CA or name C or name O or name CB )) or resid 454 through \ 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) or r \ esid 514 through 525 or (resid 526 and (name N or name CA or name C or name O or \ name CB )) or resid 527 through 577 or (resid 578 through 579 and (name N or na \ me CA or name C or name O or name CB )) or resid 580 through 582 or (resid 583 t \ hrough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 \ through 586 or (resid 587 through 588 and (name N or name CA or name C or name \ O or name CB )) or resid 589 through 609 or (resid 610 and (name N or name CA or \ name C or name O or name CB )) or resid 611 through 620 or (resid 621 and (name \ N or name CA or name C or name O or name CB )) or resid 622 through 623 or (res \ id 624 through 625 and (name N or name CA or name C or name O or name CB )) or r \ esid 626 through 648 or (resid 649 and (name N or name CA or name C or name O or \ name CB )) or resid 650 through 652 or (resid 653 and (name N or name CA or nam \ e C or name O or name CB )) or resid 654 through 658 or (resid 659 and (name N o \ r name CA or name C or name O or name CB )) or resid 660 through 664 or (resid 6 \ 65 and (name N or name CA or name C or name O or name CB )) or resid 666 through \ 668 or (resid 669 and (name N or name CA or name C or name O or name CB )) or r \ esid 670 through 680 or (resid 681 and (name N or name CA or name C or name O or \ name CB )) or resid 682 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 693 or (resid 694 through 724 a \ nd (name N or name CA or name C or name O or name CB )) or resid 725 through 733 \ or (resid 734 through 735 and (name N or name CA or name C or name O or name CB \ )) or resid 736 through 742 or (resid 743 through 746 and (name N or name CA or \ name C or name O or name CB )) or resid 747 through 786 or (resid 787 through 7 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 790 through \ 791 or (resid 792 through 793 and (name N or name CA or name C or name O or nam \ e CB )) or resid 794 or (resid 795 through 797 and (name N or name CA or name C \ or name O or name CB )) or resid 798 through 799 or (resid 800 through 806 and ( \ name N or name CA or name C or name O or name CB )) or resid 807 through 808 or \ (resid 809 and (name N or name CA or name C or name O or name CB )) or resid 810 \ or (resid 811 through 813 and (name N or name CA or name C or name O or name CB \ )) or resid 814 or (resid 815 through 816 and (name N or name CA or name C or n \ ame O or name CB )) or resid 817 through 819 or (resid 820 and (name N or name C \ A or name C or name O or name CB )) or resid 821 through 858 or (resid 859 and ( \ name N or name CA or name C or name O or name CB )) or resid 860 through 864 or \ (resid 865 through 872 and (name N or name CA or name C or name O or name CB )) \ or resid 901 through 902 or resid 904 or resid 905)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.750 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 12771 Z= 0.205 Angle : 0.614 12.938 17421 Z= 0.311 Chirality : 0.045 0.272 1991 Planarity : 0.005 0.084 2199 Dihedral : 16.875 88.301 4561 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.08 % Allowed : 29.21 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.21), residues: 1590 helix: 1.14 (0.20), residues: 679 sheet: -1.38 (0.36), residues: 203 loop : -0.84 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 299 HIS 0.002 0.000 HIS A 463 PHE 0.015 0.001 PHE B 226 TYR 0.009 0.001 TYR A 421 ARG 0.012 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 2.35719 ( 27) link_BETA1-4 : bond 0.00232 ( 4) link_BETA1-4 : angle 1.34849 ( 12) hydrogen bonds : bond 0.16547 ( 579) hydrogen bonds : angle 6.12006 ( 1665) SS BOND : bond 0.04109 ( 18) SS BOND : angle 2.15594 ( 36) covalent geometry : bond 0.00424 (12740) covalent geometry : angle 0.59947 (17346) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.343 Fit side-chains REVERT: B 525 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6614 (tm-30) REVERT: A 593 GLU cc_start: 0.7132 (pp20) cc_final: 0.6798 (pp20) REVERT: A 594 ASN cc_start: 0.5481 (m-40) cc_final: 0.5193 (p0) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 1.0699 time to fit residues: 198.2804 Evaluate side-chains 148 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 357 ASN A 592 ASN A 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.179313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126950 restraints weight = 15144.540| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.31 r_work: 0.3236 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12771 Z= 0.215 Angle : 0.601 10.185 17421 Z= 0.312 Chirality : 0.045 0.200 1991 Planarity : 0.005 0.060 2199 Dihedral : 6.855 58.901 1999 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.48 % Allowed : 25.06 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.21), residues: 1590 helix: 1.18 (0.20), residues: 693 sheet: -1.59 (0.35), residues: 218 loop : -0.85 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.004 0.001 HIS B 41 PHE 0.018 0.002 PHE B 226 TYR 0.012 0.002 TYR A 751 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 9) link_NAG-ASN : angle 2.57018 ( 27) link_BETA1-4 : bond 0.00226 ( 4) link_BETA1-4 : angle 1.48973 ( 12) hydrogen bonds : bond 0.05237 ( 579) hydrogen bonds : angle 4.95887 ( 1665) SS BOND : bond 0.00277 ( 18) SS BOND : angle 1.28743 ( 36) covalent geometry : bond 0.00509 (12740) covalent geometry : angle 0.58900 (17346) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: B 525 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6624 (tm-30) REVERT: B 551 ARG cc_start: 0.8063 (ptt90) cc_final: 0.7041 (ptt90) REVERT: B 650 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6313 (tt) REVERT: A 20 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5315 (m-80) REVERT: A 59 GLU cc_start: 0.7942 (mp0) cc_final: 0.7392 (pt0) REVERT: A 604 GLU cc_start: 0.7593 (tp30) cc_final: 0.7389 (tp30) REVERT: A 605 PHE cc_start: 0.5089 (p90) cc_final: 0.4587 (p90) REVERT: A 790 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6678 (m-80) outliers start: 55 outliers final: 26 residues processed: 193 average time/residue: 1.1278 time to fit residues: 243.6562 Evaluate side-chains 178 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120733 restraints weight = 15278.614| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.92 r_work: 0.3263 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12771 Z= 0.152 Angle : 0.552 9.924 17421 Z= 0.285 Chirality : 0.044 0.195 1991 Planarity : 0.004 0.051 2199 Dihedral : 6.294 59.227 1998 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.34 % Allowed : 25.71 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1590 helix: 1.31 (0.20), residues: 696 sheet: -1.57 (0.35), residues: 218 loop : -0.80 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 299 HIS 0.003 0.001 HIS B 41 PHE 0.015 0.001 PHE B 762 TYR 0.018 0.001 TYR A 435 ARG 0.006 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 9) link_NAG-ASN : angle 2.24209 ( 27) link_BETA1-4 : bond 0.00184 ( 4) link_BETA1-4 : angle 1.35236 ( 12) hydrogen bonds : bond 0.04588 ( 579) hydrogen bonds : angle 4.71076 ( 1665) SS BOND : bond 0.00168 ( 18) SS BOND : angle 0.90517 ( 36) covalent geometry : bond 0.00355 (12740) covalent geometry : angle 0.54349 (17346) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 416 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8458 (mm) REVERT: B 525 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6610 (tm-30) REVERT: B 551 ARG cc_start: 0.8131 (ptt90) cc_final: 0.7019 (ptt90) REVERT: A 20 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5271 (m-80) REVERT: A 59 GLU cc_start: 0.7940 (mp0) cc_final: 0.7369 (pt0) REVERT: A 61 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7261 (mt) REVERT: A 251 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 392 ARG cc_start: 0.7304 (mtp180) cc_final: 0.6927 (mtp180) REVERT: A 536 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: A 604 GLU cc_start: 0.7679 (tp30) cc_final: 0.7461 (tp30) REVERT: A 605 PHE cc_start: 0.5302 (p90) cc_final: 0.4676 (p90) REVERT: A 790 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6743 (m-80) outliers start: 41 outliers final: 20 residues processed: 178 average time/residue: 1.0582 time to fit residues: 208.5932 Evaluate side-chains 172 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 459 GLN A 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119073 restraints weight = 15180.559| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.89 r_work: 0.3233 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12771 Z= 0.217 Angle : 0.592 10.142 17421 Z= 0.307 Chirality : 0.046 0.206 1991 Planarity : 0.004 0.047 2199 Dihedral : 6.160 58.155 1998 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.80 % Allowed : 25.31 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1590 helix: 1.30 (0.20), residues: 695 sheet: -1.59 (0.34), residues: 218 loop : -0.84 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 299 HIS 0.005 0.001 HIS B 41 PHE 0.021 0.002 PHE A 814 TYR 0.013 0.002 TYR A 421 ARG 0.007 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 9) link_NAG-ASN : angle 2.64187 ( 27) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 1.54816 ( 12) hydrogen bonds : bond 0.04955 ( 579) hydrogen bonds : angle 4.75288 ( 1665) SS BOND : bond 0.00235 ( 18) SS BOND : angle 1.07993 ( 36) covalent geometry : bond 0.00516 (12740) covalent geometry : angle 0.58080 (17346) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 286 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7541 (mtm180) REVERT: B 475 GLU cc_start: 0.7630 (mm-30) cc_final: 0.6767 (mp0) REVERT: B 525 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6625 (tm-30) REVERT: B 551 ARG cc_start: 0.8162 (ptt90) cc_final: 0.7046 (ptt90) REVERT: B 650 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6261 (tt) REVERT: A 20 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.5277 (m-80) REVERT: A 59 GLU cc_start: 0.7965 (mp0) cc_final: 0.7447 (pt0) REVERT: A 61 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7328 (mt) REVERT: A 251 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7262 (mt-10) REVERT: A 270 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: A 360 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7970 (mt) REVERT: A 536 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: A 601 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.7074 (mttt) REVERT: A 604 GLU cc_start: 0.7595 (tp30) cc_final: 0.7370 (tp30) REVERT: A 605 PHE cc_start: 0.5717 (p90) cc_final: 0.4900 (p90) outliers start: 59 outliers final: 30 residues processed: 199 average time/residue: 1.1427 time to fit residues: 253.8730 Evaluate side-chains 188 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 286 ARG Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 848 LEU Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 43 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 0.0170 chunk 57 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.181203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129564 restraints weight = 15137.891| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.40 r_work: 0.3255 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12771 Z= 0.125 Angle : 0.536 9.538 17421 Z= 0.275 Chirality : 0.043 0.214 1991 Planarity : 0.004 0.042 2199 Dihedral : 5.832 57.044 1998 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.48 % Allowed : 25.31 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1590 helix: 1.51 (0.20), residues: 690 sheet: -1.53 (0.35), residues: 213 loop : -0.77 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 675 HIS 0.002 0.000 HIS B 41 PHE 0.019 0.001 PHE A 814 TYR 0.020 0.001 TYR A 435 ARG 0.008 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 9) link_NAG-ASN : angle 2.08081 ( 27) link_BETA1-4 : bond 0.00221 ( 4) link_BETA1-4 : angle 1.27072 ( 12) hydrogen bonds : bond 0.04150 ( 579) hydrogen bonds : angle 4.53591 ( 1665) SS BOND : bond 0.00141 ( 18) SS BOND : angle 0.74970 ( 36) covalent geometry : bond 0.00288 (12740) covalent geometry : angle 0.52911 (17346) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 2.263 Fit side-chains revert: symmetry clash REVERT: B 475 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6816 (mp0) REVERT: B 519 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: B 525 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6550 (tm-30) REVERT: B 551 ARG cc_start: 0.8144 (ptt90) cc_final: 0.7057 (ptt90) REVERT: B 650 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6331 (tt) REVERT: A 59 GLU cc_start: 0.7990 (mp0) cc_final: 0.7450 (pt0) REVERT: A 61 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 205 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8152 (mpt-90) REVERT: A 251 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7262 (mt-10) REVERT: A 270 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: A 392 ARG cc_start: 0.7348 (mtp180) cc_final: 0.7009 (mtp180) REVERT: A 601 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7119 (mttt) REVERT: A 605 PHE cc_start: 0.5779 (p90) cc_final: 0.4979 (p90) outliers start: 55 outliers final: 23 residues processed: 193 average time/residue: 1.5914 time to fit residues: 341.1576 Evaluate side-chains 172 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 90 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 125 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.181019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128390 restraints weight = 15451.542| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.25 r_work: 0.3285 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12771 Z= 0.137 Angle : 0.545 9.488 17421 Z= 0.279 Chirality : 0.043 0.227 1991 Planarity : 0.004 0.041 2199 Dihedral : 5.728 55.936 1998 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.42 % Allowed : 26.53 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1590 helix: 1.54 (0.20), residues: 693 sheet: -1.58 (0.35), residues: 218 loop : -0.78 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 675 HIS 0.003 0.001 HIS B 41 PHE 0.020 0.001 PHE A 814 TYR 0.010 0.001 TYR B 421 ARG 0.009 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 9) link_NAG-ASN : angle 2.12778 ( 27) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.33862 ( 12) hydrogen bonds : bond 0.04172 ( 579) hydrogen bonds : angle 4.48711 ( 1665) SS BOND : bond 0.00145 ( 18) SS BOND : angle 0.79262 ( 36) covalent geometry : bond 0.00319 (12740) covalent geometry : angle 0.53774 (17346) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 416 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8391 (mm) REVERT: B 475 GLU cc_start: 0.7706 (mm-30) cc_final: 0.6842 (mp0) REVERT: B 519 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: B 525 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 650 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6370 (tt) REVERT: A 59 GLU cc_start: 0.7955 (mp0) cc_final: 0.7375 (pt0) REVERT: A 251 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 270 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: A 392 ARG cc_start: 0.7312 (mtp180) cc_final: 0.6968 (mtp180) REVERT: A 604 GLU cc_start: 0.7465 (tp30) cc_final: 0.7263 (tp30) REVERT: A 605 PHE cc_start: 0.5614 (p90) cc_final: 0.5020 (p90) outliers start: 42 outliers final: 26 residues processed: 184 average time/residue: 1.0204 time to fit residues: 208.6114 Evaluate side-chains 180 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 154 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN A 357 ASN A 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.180364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128378 restraints weight = 15300.535| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.39 r_work: 0.3242 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12771 Z= 0.160 Angle : 0.561 9.416 17421 Z= 0.288 Chirality : 0.044 0.244 1991 Planarity : 0.004 0.041 2199 Dihedral : 5.731 56.080 1998 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.07 % Allowed : 26.12 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1590 helix: 1.49 (0.20), residues: 694 sheet: -1.58 (0.34), residues: 218 loop : -0.78 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 675 HIS 0.003 0.001 HIS B 41 PHE 0.024 0.001 PHE A 814 TYR 0.020 0.001 TYR A 435 ARG 0.010 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 9) link_NAG-ASN : angle 2.26223 ( 27) link_BETA1-4 : bond 0.00200 ( 4) link_BETA1-4 : angle 1.37922 ( 12) hydrogen bonds : bond 0.04343 ( 579) hydrogen bonds : angle 4.53548 ( 1665) SS BOND : bond 0.00157 ( 18) SS BOND : angle 0.89354 ( 36) covalent geometry : bond 0.00378 (12740) covalent geometry : angle 0.55225 (17346) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 416 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 475 GLU cc_start: 0.7740 (mm-30) cc_final: 0.6859 (mp0) REVERT: B 519 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: B 525 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6638 (tm-30) REVERT: B 650 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6353 (tt) REVERT: B 673 GLN cc_start: 0.5284 (OUTLIER) cc_final: 0.4827 (mp-120) REVERT: B 829 TYR cc_start: 0.5982 (OUTLIER) cc_final: 0.5525 (t80) REVERT: A 20 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: A 59 GLU cc_start: 0.7951 (mp0) cc_final: 0.7395 (pt0) REVERT: A 251 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 270 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: A 392 ARG cc_start: 0.7300 (mtp180) cc_final: 0.6947 (mtp180) REVERT: A 401 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7578 (mt) REVERT: A 536 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 580 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 604 GLU cc_start: 0.7449 (tp30) cc_final: 0.7216 (tp30) REVERT: A 605 PHE cc_start: 0.5683 (p90) cc_final: 0.5011 (p90) outliers start: 50 outliers final: 27 residues processed: 196 average time/residue: 1.0323 time to fit residues: 224.7546 Evaluate side-chains 188 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 673 GLN Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 829 TYR Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.178596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126295 restraints weight = 15359.155| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.48 r_work: 0.3210 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12771 Z= 0.234 Angle : 0.623 10.243 17421 Z= 0.321 Chirality : 0.046 0.257 1991 Planarity : 0.004 0.042 2199 Dihedral : 5.949 56.062 1998 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.82 % Allowed : 26.69 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1590 helix: 1.35 (0.19), residues: 694 sheet: -1.57 (0.34), residues: 216 loop : -0.85 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 675 HIS 0.004 0.001 HIS A 463 PHE 0.020 0.002 PHE A 814 TYR 0.020 0.002 TYR A 435 ARG 0.011 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 9) link_NAG-ASN : angle 2.69389 ( 27) link_BETA1-4 : bond 0.00415 ( 4) link_BETA1-4 : angle 1.58881 ( 12) hydrogen bonds : bond 0.04915 ( 579) hydrogen bonds : angle 4.70814 ( 1665) SS BOND : bond 0.00239 ( 18) SS BOND : angle 1.11451 ( 36) covalent geometry : bond 0.00559 (12740) covalent geometry : angle 0.61142 (17346) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7625 (mt-10) REVERT: B 475 GLU cc_start: 0.7713 (mm-30) cc_final: 0.6808 (mp0) REVERT: B 525 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6654 (tm-30) REVERT: B 650 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6311 (tt) REVERT: B 754 GLN cc_start: 0.7920 (pt0) cc_final: 0.7377 (pt0) REVERT: A 20 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: A 251 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 270 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: A 392 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6946 (mtp180) REVERT: A 401 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7617 (mt) REVERT: A 536 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: A 604 GLU cc_start: 0.7526 (tp30) cc_final: 0.7270 (tp30) REVERT: A 605 PHE cc_start: 0.5893 (p90) cc_final: 0.5152 (p90) outliers start: 47 outliers final: 29 residues processed: 188 average time/residue: 0.9877 time to fit residues: 206.9663 Evaluate side-chains 184 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN A 357 ASN A 753 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127048 restraints weight = 15314.311| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.33 r_work: 0.3247 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12771 Z= 0.172 Angle : 0.589 9.963 17421 Z= 0.302 Chirality : 0.045 0.266 1991 Planarity : 0.004 0.041 2199 Dihedral : 5.813 54.556 1998 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.66 % Allowed : 27.01 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1590 helix: 1.41 (0.19), residues: 694 sheet: -1.61 (0.34), residues: 217 loop : -0.80 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 675 HIS 0.004 0.001 HIS B 41 PHE 0.026 0.002 PHE A 814 TYR 0.021 0.002 TYR A 435 ARG 0.011 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 9) link_NAG-ASN : angle 2.37310 ( 27) link_BETA1-4 : bond 0.00217 ( 4) link_BETA1-4 : angle 1.38612 ( 12) hydrogen bonds : bond 0.04453 ( 579) hydrogen bonds : angle 4.61523 ( 1665) SS BOND : bond 0.00175 ( 18) SS BOND : angle 0.90334 ( 36) covalent geometry : bond 0.00407 (12740) covalent geometry : angle 0.58016 (17346) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7949 (mmt) REVERT: B 270 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: B 475 GLU cc_start: 0.7735 (mm-30) cc_final: 0.6816 (mp0) REVERT: B 525 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6546 (tm-30) REVERT: B 650 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6326 (tt) REVERT: B 829 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5376 (t80) REVERT: A 20 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5408 (m-80) REVERT: A 59 GLU cc_start: 0.7953 (mp0) cc_final: 0.7390 (pt0) REVERT: A 251 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7246 (mt-10) REVERT: A 270 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: A 392 ARG cc_start: 0.7358 (mtp180) cc_final: 0.6984 (mtp180) REVERT: A 536 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: A 580 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8471 (p) REVERT: A 604 GLU cc_start: 0.7493 (tp30) cc_final: 0.7231 (tp30) REVERT: A 605 PHE cc_start: 0.5825 (p90) cc_final: 0.5057 (p90) outliers start: 45 outliers final: 28 residues processed: 182 average time/residue: 1.1601 time to fit residues: 234.2865 Evaluate side-chains 185 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 829 TYR Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120674 restraints weight = 15304.139| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.90 r_work: 0.3249 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12771 Z= 0.163 Angle : 0.588 9.889 17421 Z= 0.300 Chirality : 0.045 0.271 1991 Planarity : 0.004 0.041 2199 Dihedral : 5.732 53.013 1998 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.25 % Allowed : 27.66 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1590 helix: 1.45 (0.19), residues: 694 sheet: -1.58 (0.34), residues: 217 loop : -0.79 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 675 HIS 0.003 0.001 HIS B 41 PHE 0.018 0.001 PHE A 814 TYR 0.011 0.001 TYR A 421 ARG 0.012 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 9) link_NAG-ASN : angle 2.28834 ( 27) link_BETA1-4 : bond 0.00201 ( 4) link_BETA1-4 : angle 1.39638 ( 12) hydrogen bonds : bond 0.04380 ( 579) hydrogen bonds : angle 4.58486 ( 1665) SS BOND : bond 0.00163 ( 18) SS BOND : angle 0.87731 ( 36) covalent geometry : bond 0.00387 (12740) covalent geometry : angle 0.58019 (17346) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.437 Fit side-chains revert: symmetry clash REVERT: B 197 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7935 (mmt) REVERT: B 270 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: B 475 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6820 (mp0) REVERT: B 525 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6531 (tm-30) REVERT: B 650 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6269 (tt) REVERT: B 754 GLN cc_start: 0.7906 (pt0) cc_final: 0.7379 (pt0) REVERT: B 829 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.5433 (t80) REVERT: A 20 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: A 59 GLU cc_start: 0.7927 (mp0) cc_final: 0.7389 (pt0) REVERT: A 251 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 270 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: A 392 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6931 (mtp180) REVERT: A 536 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7742 (pt0) REVERT: A 580 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 604 GLU cc_start: 0.7439 (tp30) cc_final: 0.7134 (tp30) REVERT: A 605 PHE cc_start: 0.5752 (p90) cc_final: 0.5013 (p90) outliers start: 40 outliers final: 29 residues processed: 175 average time/residue: 0.9758 time to fit residues: 190.2011 Evaluate side-chains 183 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 734 MET Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 829 TYR Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 790 PHE Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 857 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 753 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127423 restraints weight = 15300.619| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.30 r_work: 0.3246 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12771 Z= 0.177 Angle : 0.595 10.429 17421 Z= 0.303 Chirality : 0.045 0.270 1991 Planarity : 0.004 0.041 2199 Dihedral : 5.745 52.939 1998 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.42 % Allowed : 27.50 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1590 helix: 1.43 (0.19), residues: 694 sheet: -1.58 (0.34), residues: 217 loop : -0.81 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 675 HIS 0.004 0.001 HIS B 41 PHE 0.030 0.002 PHE A 814 TYR 0.022 0.002 TYR A 435 ARG 0.012 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 9) link_NAG-ASN : angle 2.37327 ( 27) link_BETA1-4 : bond 0.00238 ( 4) link_BETA1-4 : angle 1.43665 ( 12) hydrogen bonds : bond 0.04468 ( 579) hydrogen bonds : angle 4.60658 ( 1665) SS BOND : bond 0.00172 ( 18) SS BOND : angle 0.92497 ( 36) covalent geometry : bond 0.00421 (12740) covalent geometry : angle 0.58618 (17346) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11530.06 seconds wall clock time: 205 minutes 1.38 seconds (12301.38 seconds total)