Starting phenix.real_space_refine on Fri Mar 6 22:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rl7_24519/03_2026/7rl7_24519.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rl7_24519/03_2026/7rl7_24519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rl7_24519/03_2026/7rl7_24519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rl7_24519/03_2026/7rl7_24519.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rl7_24519/03_2026/7rl7_24519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rl7_24519/03_2026/7rl7_24519.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21882 2.51 5 N 6138 2.21 5 O 6690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34950 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5761 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.62, per 1000 atoms: 0.22 Number of scatterers: 34950 At special positions: 0 Unit cell: (163.013, 175.163, 118.463, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6690 8.00 N 6138 7.00 C 21882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 24 sheets defined 46.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 85 through 90 removed outlier: 4.120A pdb=" N VAL A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN A 90 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.514A pdb=" N GLU A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.645A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.773A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.868A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.674A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.890A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 4.003A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.582A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.791A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.544A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.977A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.588A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.895A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.679A pdb=" N ASN A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.537A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.985A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.585A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 707 removed outlier: 3.913A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.597A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.806A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.714A pdb=" N ARG A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 85 through 90 removed outlier: 4.119A pdb=" N VAL B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN B 90 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.514A pdb=" N GLU B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.645A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.774A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.868A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.675A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.889A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 335 removed outlier: 4.003A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.581A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.791A pdb=" N GLN B 458 " --> pdb=" O TRP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.544A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.977A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.588A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 578 through 585 removed outlier: 3.895A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.679A pdb=" N ASN B 602 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.536A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.986A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.586A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 707 removed outlier: 3.913A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.596A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 removed outlier: 3.806A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.713A pdb=" N ARG B 766 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 85 through 90 removed outlier: 4.120A pdb=" N VAL C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN C 90 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 199 removed outlier: 3.515A pdb=" N GLU C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.644A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 220 through 226 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.774A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.868A pdb=" N ASN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.675A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.890A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 335 removed outlier: 4.003A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.581A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.791A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.544A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.977A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.588A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 559 through 569 Processing helix chain 'C' and resid 578 through 585 removed outlier: 3.894A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 611 removed outlier: 3.679A pdb=" N ASN C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.536A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.986A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.585A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 707 removed outlier: 3.913A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 742 removed outlier: 3.597A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 3.805A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 761 " --> pdb=" O MET C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.713A pdb=" N ARG C 766 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 85 through 90 removed outlier: 4.120A pdb=" N VAL D 88 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN D 90 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 199 removed outlier: 3.514A pdb=" N GLU D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.645A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 220 through 226 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.773A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.869A pdb=" N ASN D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.674A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.889A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 335 removed outlier: 4.003A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.581A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.791A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 4.544A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.978A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.589A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'D' and resid 578 through 585 removed outlier: 3.894A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.679A pdb=" N ASN D 602 " --> pdb=" O ASP D 598 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.537A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.986A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.586A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 707 removed outlier: 3.913A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.597A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 removed outlier: 3.806A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.713A pdb=" N ARG D 766 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 85 through 90 removed outlier: 4.120A pdb=" N VAL E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN E 90 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.514A pdb=" N GLU E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.644A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 220 through 226 Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.772A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.868A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.675A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.890A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 removed outlier: 4.003A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.581A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.791A pdb=" N GLN E 458 " --> pdb=" O TRP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.544A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 507 removed outlier: 3.978A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.587A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 550 Processing helix chain 'E' and resid 559 through 569 Processing helix chain 'E' and resid 578 through 585 removed outlier: 3.895A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 611 removed outlier: 3.679A pdb=" N ASN E 602 " --> pdb=" O ASP E 598 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN E 603 " --> pdb=" O ARG E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.537A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.987A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.586A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 707 removed outlier: 3.913A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.598A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 removed outlier: 3.805A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 761 " --> pdb=" O MET E 757 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 766 removed outlier: 3.714A pdb=" N ARG E 766 " --> pdb=" O GLN E 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 18 Processing helix chain 'F' and resid 42 through 47 Processing helix chain 'F' and resid 85 through 90 removed outlier: 4.120A pdb=" N VAL F 88 " --> pdb=" O ASN F 85 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN F 90 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.514A pdb=" N GLU F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.644A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.773A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 removed outlier: 3.868A pdb=" N ASN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.675A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.890A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 4.003A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.581A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.791A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.544A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 507 removed outlier: 3.977A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.588A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 550 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'F' and resid 578 through 585 removed outlier: 3.894A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 611 removed outlier: 3.679A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN F 603 " --> pdb=" O ARG F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.537A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.986A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.586A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 707 removed outlier: 3.912A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.596A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 removed outlier: 3.805A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 761 " --> pdb=" O MET F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 766 removed outlier: 3.713A pdb=" N ARG F 766 " --> pdb=" O GLN F 763 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.103A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.713A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.796A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 59 through 60 Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 153 removed outlier: 4.104A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.711A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.795A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB1, first strand: chain 'C' and resid 152 through 153 removed outlier: 4.103A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.712A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.794A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AB5, first strand: chain 'D' and resid 152 through 153 removed outlier: 4.103A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.712A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.795A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 59 through 60 Processing sheet with id=AB9, first strand: chain 'E' and resid 152 through 153 removed outlier: 4.103A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.712A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.795A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 59 through 60 Processing sheet with id=AC4, first strand: chain 'F' and resid 152 through 153 removed outlier: 4.104A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.712A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.795A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1264 hydrogen bonds defined for protein. 3546 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: 6.52 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 12100 1.37 - 1.52: 9725 1.52 - 1.66: 13401 1.66 - 1.80: 191 1.80 - 1.95: 109 Bond restraints: 35526 Sorted by residual: bond pdb=" CA PHE F 163 " pdb=" CB PHE F 163 " ideal model delta sigma weight residual 1.533 1.562 -0.029 1.72e-02 3.38e+03 2.77e+00 bond pdb=" CA PHE A 163 " pdb=" CB PHE A 163 " ideal model delta sigma weight residual 1.533 1.562 -0.028 1.72e-02 3.38e+03 2.72e+00 bond pdb=" CA PHE E 163 " pdb=" CB PHE E 163 " ideal model delta sigma weight residual 1.533 1.562 -0.028 1.72e-02 3.38e+03 2.71e+00 bond pdb=" CA PHE D 163 " pdb=" CB PHE D 163 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.72e-02 3.38e+03 2.66e+00 bond pdb=" CA PHE B 163 " pdb=" CB PHE B 163 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.72e-02 3.38e+03 2.65e+00 ... (remaining 35521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 47307 2.25 - 4.50: 645 4.50 - 6.75: 72 6.75 - 9.00: 18 9.00 - 11.25: 18 Bond angle restraints: 48060 Sorted by residual: angle pdb=" N VAL B 94 " pdb=" CA VAL B 94 " pdb=" C VAL B 94 " ideal model delta sigma weight residual 113.71 109.77 3.94 9.50e-01 1.11e+00 1.72e+01 angle pdb=" CB MET F 678 " pdb=" CG MET F 678 " pdb=" SD MET F 678 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET D 678 " pdb=" CG MET D 678 " pdb=" SD MET D 678 " ideal model delta sigma weight residual 112.70 123.94 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CB MET E 678 " pdb=" CG MET E 678 " pdb=" SD MET E 678 " ideal model delta sigma weight residual 112.70 123.94 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CB MET C 678 " pdb=" CG MET C 678 " pdb=" SD MET C 678 " ideal model delta sigma weight residual 112.70 123.92 -11.22 3.00e+00 1.11e-01 1.40e+01 ... (remaining 48055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 18948 16.04 - 32.09: 2178 32.09 - 48.13: 726 48.13 - 64.17: 156 64.17 - 80.22: 42 Dihedral angle restraints: 22050 sinusoidal: 9330 harmonic: 12720 Sorted by residual: dihedral pdb=" CA ARG B 599 " pdb=" C ARG B 599 " pdb=" N VAL B 600 " pdb=" CA VAL B 600 " ideal model delta harmonic sigma weight residual -180.00 -164.48 -15.52 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CA ARG D 599 " pdb=" C ARG D 599 " pdb=" N VAL D 600 " pdb=" CA VAL D 600 " ideal model delta harmonic sigma weight residual -180.00 -164.50 -15.50 0 5.00e+00 4.00e-02 9.61e+00 dihedral pdb=" CA ARG E 599 " pdb=" C ARG E 599 " pdb=" N VAL E 600 " pdb=" CA VAL E 600 " ideal model delta harmonic sigma weight residual -180.00 -164.50 -15.50 0 5.00e+00 4.00e-02 9.61e+00 ... (remaining 22047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3739 0.040 - 0.081: 1228 0.081 - 0.121: 421 0.121 - 0.162: 42 0.162 - 0.202: 6 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CB ILE A 590 " pdb=" CA ILE A 590 " pdb=" CG1 ILE A 590 " pdb=" CG2 ILE A 590 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE F 590 " pdb=" CA ILE F 590 " pdb=" CG1 ILE F 590 " pdb=" CG2 ILE F 590 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE E 590 " pdb=" CA ILE E 590 " pdb=" CG1 ILE E 590 " pdb=" CG2 ILE E 590 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 5433 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 297 " -0.044 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO D 298 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 298 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 298 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " 0.044 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO B 298 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 297 " -0.044 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO E 298 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " -0.038 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 509 2.63 - 3.19: 30807 3.19 - 3.76: 54313 3.76 - 4.33: 73360 4.33 - 4.90: 118544 Nonbonded interactions: 277533 Sorted by model distance: nonbonded pdb=" OG1 THR F 252 " pdb="MG MG F 903 " model vdw 2.057 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR B 252 " pdb="MG MG B 903 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR A 252 " pdb="MG MG A 903 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 2.059 2.170 ... (remaining 277528 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.770 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35526 Z= 0.145 Angle : 0.683 11.251 48060 Z= 0.378 Chirality : 0.044 0.202 5436 Planarity : 0.003 0.068 6288 Dihedral : 15.608 80.215 13806 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 21.35 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 4398 helix: 0.34 (0.13), residues: 1746 sheet: 0.29 (0.27), residues: 372 loop : -1.84 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 424 TYR 0.008 0.001 TYR F 755 PHE 0.014 0.001 PHE D 758 TRP 0.026 0.004 TRP E 551 HIS 0.003 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00300 (35526) covalent geometry : angle 0.68286 (48060) hydrogen bonds : bond 0.21043 ( 1264) hydrogen bonds : angle 6.03300 ( 3546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.275 Fit side-chains REVERT: A 508 MET cc_start: 0.8280 (mmt) cc_final: 0.8008 (mmt) REVERT: D 163 PHE cc_start: 0.7301 (t80) cc_final: 0.7074 (t80) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.6985 time to fit residues: 175.0130 Evaluate side-chains 184 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.0370 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0170 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 0.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 406 HIS B 406 HIS C 406 HIS D 296 ASN D 406 HIS E 406 HIS F 406 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.126882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.077608 restraints weight = 70239.987| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.48 r_work: 0.2859 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35526 Z= 0.119 Angle : 0.565 8.605 48060 Z= 0.280 Chirality : 0.044 0.188 5436 Planarity : 0.003 0.031 6288 Dihedral : 6.434 49.819 5022 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.61 % Allowed : 19.06 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4398 helix: 0.66 (0.13), residues: 1770 sheet: 0.11 (0.27), residues: 378 loop : -1.69 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.008 0.001 TYR E 138 PHE 0.015 0.001 PHE F 163 TRP 0.021 0.003 TRP B 551 HIS 0.002 0.001 HIS F 317 Details of bonding type rmsd covalent geometry : bond 0.00275 (35526) covalent geometry : angle 0.56473 (48060) hydrogen bonds : bond 0.03788 ( 1264) hydrogen bonds : angle 4.32950 ( 3546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 197 time to evaluate : 1.389 Fit side-chains REVERT: A 158 MET cc_start: 0.5181 (pmm) cc_final: 0.4927 (pmm) REVERT: A 163 PHE cc_start: 0.6986 (t80) cc_final: 0.6567 (t80) REVERT: B 158 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5305 (pmm) REVERT: B 437 ILE cc_start: 0.5738 (OUTLIER) cc_final: 0.5491 (mp) REVERT: C 158 MET cc_start: 0.4669 (pmm) cc_final: 0.4394 (pmm) REVERT: C 437 ILE cc_start: 0.6142 (OUTLIER) cc_final: 0.5861 (mp) REVERT: D 158 MET cc_start: 0.4966 (pmm) cc_final: 0.4613 (pmm) REVERT: D 163 PHE cc_start: 0.7271 (t80) cc_final: 0.6730 (t80) REVERT: D 437 ILE cc_start: 0.5849 (OUTLIER) cc_final: 0.5511 (mp) REVERT: E 158 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.5242 (ppp) REVERT: E 437 ILE cc_start: 0.5914 (OUTLIER) cc_final: 0.5694 (mp) REVERT: F 158 MET cc_start: 0.4911 (pmm) cc_final: 0.4633 (pmm) outliers start: 98 outliers final: 17 residues processed: 282 average time/residue: 0.6454 time to fit residues: 223.5568 Evaluate side-chains 209 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 133 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 339 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 373 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.122934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.072585 restraints weight = 70035.899| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.94 r_work: 0.2677 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 35526 Z= 0.239 Angle : 0.620 8.289 48060 Z= 0.306 Chirality : 0.047 0.162 5436 Planarity : 0.004 0.041 6288 Dihedral : 6.654 52.668 5022 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.90 % Allowed : 19.12 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4398 helix: 0.74 (0.13), residues: 1764 sheet: -0.21 (0.25), residues: 390 loop : -1.65 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 741 TYR 0.010 0.001 TYR E 138 PHE 0.018 0.002 PHE B 742 TRP 0.025 0.004 TRP B 551 HIS 0.005 0.001 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00563 (35526) covalent geometry : angle 0.61951 (48060) hydrogen bonds : bond 0.03827 ( 1264) hydrogen bonds : angle 4.19228 ( 3546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 181 time to evaluate : 1.326 Fit side-chains REVERT: A 59 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8001 (tm) REVERT: A 158 MET cc_start: 0.5245 (pmm) cc_final: 0.4879 (pmm) REVERT: A 163 PHE cc_start: 0.6906 (t80) cc_final: 0.6542 (t80) REVERT: A 281 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7827 (tp30) REVERT: B 158 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5227 (ppp) REVERT: B 163 PHE cc_start: 0.6765 (t80) cc_final: 0.6337 (t80) REVERT: B 758 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.7724 (t80) REVERT: C 158 MET cc_start: 0.4882 (pmm) cc_final: 0.4671 (pmm) REVERT: C 437 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6360 (mp) REVERT: C 758 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.7534 (t80) REVERT: D 59 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (tm) REVERT: D 158 MET cc_start: 0.5222 (pmm) cc_final: 0.4927 (pmm) REVERT: D 163 PHE cc_start: 0.7011 (t80) cc_final: 0.6534 (t80) REVERT: E 158 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5347 (ppp) REVERT: E 281 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: E 437 ILE cc_start: 0.6586 (OUTLIER) cc_final: 0.6372 (mp) REVERT: E 758 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.7636 (t80) REVERT: F 158 MET cc_start: 0.5091 (pmm) cc_final: 0.4722 (pmm) REVERT: F 173 TYR cc_start: 0.4892 (OUTLIER) cc_final: 0.3232 (p90) REVERT: F 437 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.6070 (mp) REVERT: F 758 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.7551 (t80) outliers start: 109 outliers final: 36 residues processed: 277 average time/residue: 0.6418 time to fit residues: 217.0108 Evaluate side-chains 222 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 7 optimal weight: 40.0000 chunk 393 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 371 optimal weight: 8.9990 chunk 357 optimal weight: 0.4980 chunk 331 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 296 ASN C 296 ASN D 327 GLN E 296 ASN E 327 GLN F 296 ASN F 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.124323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075039 restraints weight = 69273.233| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.87 r_work: 0.2731 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35526 Z= 0.123 Angle : 0.543 9.124 48060 Z= 0.264 Chirality : 0.044 0.146 5436 Planarity : 0.003 0.035 6288 Dihedral : 6.570 55.575 5022 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.64 % Allowed : 19.76 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4398 helix: 0.94 (0.13), residues: 1764 sheet: -0.28 (0.26), residues: 396 loop : -1.51 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 225 TYR 0.008 0.001 TYR E 138 PHE 0.015 0.001 PHE B 742 TRP 0.023 0.002 TRP B 551 HIS 0.002 0.000 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00291 (35526) covalent geometry : angle 0.54314 (48060) hydrogen bonds : bond 0.03122 ( 1264) hydrogen bonds : angle 3.99530 ( 3546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 175 time to evaluate : 1.390 Fit side-chains REVERT: A 59 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8128 (tm) REVERT: A 158 MET cc_start: 0.4969 (pmm) cc_final: 0.4558 (pmm) REVERT: A 163 PHE cc_start: 0.6961 (t80) cc_final: 0.6498 (t80) REVERT: B 158 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.5403 (ppp) REVERT: B 163 PHE cc_start: 0.6914 (t80) cc_final: 0.6303 (t80) REVERT: B 758 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.7496 (t80) REVERT: C 158 MET cc_start: 0.5001 (pmm) cc_final: 0.4750 (pmm) REVERT: C 437 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6532 (mp) REVERT: C 758 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.7570 (t80) REVERT: D 59 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8099 (tm) REVERT: D 158 MET cc_start: 0.5011 (pmm) cc_final: 0.4610 (pmm) REVERT: D 163 PHE cc_start: 0.6942 (t80) cc_final: 0.6632 (t80) REVERT: D 508 MET cc_start: 0.8735 (mmt) cc_final: 0.8403 (mmt) REVERT: E 158 MET cc_start: 0.5631 (OUTLIER) cc_final: 0.5330 (ppp) REVERT: E 758 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7547 (t80) REVERT: F 158 MET cc_start: 0.5104 (pmm) cc_final: 0.4705 (pmm) REVERT: F 219 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8845 (ptm) REVERT: F 758 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.7600 (t80) outliers start: 99 outliers final: 40 residues processed: 257 average time/residue: 0.6192 time to fit residues: 197.0233 Evaluate side-chains 222 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 70 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 433 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 213 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.123950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074389 restraints weight = 69617.457| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.84 r_work: 0.2720 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35526 Z= 0.137 Angle : 0.547 9.436 48060 Z= 0.263 Chirality : 0.044 0.141 5436 Planarity : 0.003 0.036 6288 Dihedral : 6.532 56.163 5022 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.85 % Allowed : 19.83 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4398 helix: 1.08 (0.13), residues: 1764 sheet: -0.33 (0.26), residues: 396 loop : -1.40 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 225 TYR 0.007 0.001 TYR D 138 PHE 0.020 0.001 PHE A 742 TRP 0.027 0.003 TRP B 551 HIS 0.002 0.001 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00325 (35526) covalent geometry : angle 0.54664 (48060) hydrogen bonds : bond 0.03009 ( 1264) hydrogen bonds : angle 3.89936 ( 3546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 179 time to evaluate : 1.418 Fit side-chains REVERT: A 59 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8137 (tm) REVERT: A 158 MET cc_start: 0.5012 (pmm) cc_final: 0.4586 (pmm) REVERT: A 163 PHE cc_start: 0.6833 (t80) cc_final: 0.6261 (t80) REVERT: A 508 MET cc_start: 0.8721 (mmt) cc_final: 0.8461 (mmt) REVERT: B 158 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.5059 (pmm) REVERT: B 163 PHE cc_start: 0.7023 (t80) cc_final: 0.6467 (t80) REVERT: B 369 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8787 (mm) REVERT: B 561 GLU cc_start: 0.7846 (pm20) cc_final: 0.7570 (pm20) REVERT: B 758 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7598 (t80) REVERT: C 158 MET cc_start: 0.5080 (pmm) cc_final: 0.4816 (pmm) REVERT: C 437 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6738 (mp) REVERT: C 758 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.7602 (t80) REVERT: D 59 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8153 (tm) REVERT: D 158 MET cc_start: 0.4999 (pmm) cc_final: 0.4586 (pmm) REVERT: D 163 PHE cc_start: 0.6949 (t80) cc_final: 0.6693 (t80) REVERT: E 158 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5321 (ppp) REVERT: E 369 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8795 (mm) REVERT: E 758 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.7519 (t80) REVERT: F 158 MET cc_start: 0.5195 (pmm) cc_final: 0.4770 (pmm) REVERT: F 219 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8833 (ptm) REVERT: F 758 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.7518 (t80) outliers start: 107 outliers final: 50 residues processed: 264 average time/residue: 0.6229 time to fit residues: 203.4957 Evaluate side-chains 237 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 634 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 166 optimal weight: 0.9980 chunk 333 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 356 optimal weight: 0.9980 chunk 427 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 382 optimal weight: 0.0870 chunk 136 optimal weight: 0.7980 chunk 380 optimal weight: 50.0000 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.124528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.074520 restraints weight = 69447.363| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.95 r_work: 0.2744 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35526 Z= 0.111 Angle : 0.533 10.540 48060 Z= 0.254 Chirality : 0.043 0.140 5436 Planarity : 0.003 0.037 6288 Dihedral : 6.465 56.735 5022 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.56 % Allowed : 20.55 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4398 helix: 1.14 (0.13), residues: 1770 sheet: -0.29 (0.26), residues: 396 loop : -1.32 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 225 TYR 0.006 0.001 TYR D 138 PHE 0.016 0.001 PHE F 742 TRP 0.031 0.003 TRP F 551 HIS 0.002 0.000 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00264 (35526) covalent geometry : angle 0.53263 (48060) hydrogen bonds : bond 0.02797 ( 1264) hydrogen bonds : angle 3.78777 ( 3546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 179 time to evaluate : 1.349 Fit side-chains REVERT: A 59 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8098 (tm) REVERT: A 158 MET cc_start: 0.5116 (pmm) cc_final: 0.4686 (pmm) REVERT: A 163 PHE cc_start: 0.6787 (t80) cc_final: 0.6147 (t80) REVERT: A 508 MET cc_start: 0.8664 (mmt) cc_final: 0.8339 (mmt) REVERT: B 158 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.5213 (ppp) REVERT: B 163 PHE cc_start: 0.6934 (t80) cc_final: 0.6416 (t80) REVERT: B 561 GLU cc_start: 0.7809 (pm20) cc_final: 0.7494 (pm20) REVERT: B 758 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7525 (t80) REVERT: C 758 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.7518 (t80) REVERT: D 59 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (tm) REVERT: D 158 MET cc_start: 0.4791 (pmm) cc_final: 0.4443 (pmm) REVERT: D 163 PHE cc_start: 0.6906 (t80) cc_final: 0.6679 (t80) REVERT: E 158 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.5195 (ppp) REVERT: E 758 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.7500 (t80) REVERT: F 158 MET cc_start: 0.5264 (pmm) cc_final: 0.4831 (pmm) REVERT: F 758 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.7575 (t80) outliers start: 96 outliers final: 51 residues processed: 256 average time/residue: 0.6417 time to fit residues: 203.3506 Evaluate side-chains 235 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 0.0870 chunk 419 optimal weight: 10.0000 chunk 330 optimal weight: 0.9990 chunk 425 optimal weight: 2.9990 chunk 152 optimal weight: 30.0000 chunk 362 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 chunk 155 optimal weight: 30.0000 chunk 239 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.122695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073628 restraints weight = 69637.316| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.96 r_work: 0.2694 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35526 Z= 0.177 Angle : 0.585 10.855 48060 Z= 0.278 Chirality : 0.045 0.141 5436 Planarity : 0.003 0.037 6288 Dihedral : 6.613 55.113 5022 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.61 % Allowed : 20.53 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 4398 helix: 1.18 (0.13), residues: 1764 sheet: -0.29 (0.26), residues: 396 loop : -1.24 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 560 TYR 0.009 0.001 TYR B 138 PHE 0.022 0.001 PHE A 742 TRP 0.037 0.004 TRP B 551 HIS 0.004 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00417 (35526) covalent geometry : angle 0.58460 (48060) hydrogen bonds : bond 0.03111 ( 1264) hydrogen bonds : angle 3.88331 ( 3546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 171 time to evaluate : 1.197 Fit side-chains REVERT: A 59 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8183 (tm) REVERT: A 158 MET cc_start: 0.5124 (pmm) cc_final: 0.4845 (pmm) REVERT: A 163 PHE cc_start: 0.6824 (t80) cc_final: 0.6203 (t80) REVERT: A 508 MET cc_start: 0.8699 (mmt) cc_final: 0.8347 (mmt) REVERT: B 158 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.5024 (pmm) REVERT: B 163 PHE cc_start: 0.6813 (t80) cc_final: 0.6321 (t80) REVERT: B 369 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8837 (mm) REVERT: B 561 GLU cc_start: 0.7910 (pm20) cc_final: 0.7580 (pm20) REVERT: B 758 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.7601 (t80) REVERT: C 46 MET cc_start: 0.5949 (tpt) cc_final: 0.5679 (tpt) REVERT: C 158 MET cc_start: 0.5044 (pmm) cc_final: 0.4481 (pmm) REVERT: C 758 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.7599 (t80) REVERT: D 59 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8195 (tm) REVERT: D 158 MET cc_start: 0.4685 (pmm) cc_final: 0.4319 (pmm) REVERT: D 163 PHE cc_start: 0.6945 (t80) cc_final: 0.6728 (t80) REVERT: E 158 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5379 (ppp) REVERT: E 369 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8850 (mm) REVERT: E 758 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.7566 (t80) REVERT: F 158 MET cc_start: 0.5134 (pmm) cc_final: 0.4907 (pmm) REVERT: F 758 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 98 outliers final: 51 residues processed: 254 average time/residue: 0.6863 time to fit residues: 212.4355 Evaluate side-chains 231 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 468 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 92 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 0.6980 chunk 355 optimal weight: 0.0870 chunk 295 optimal weight: 0.0370 chunk 364 optimal weight: 6.9990 chunk 385 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 281 optimal weight: 0.0370 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.124807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076156 restraints weight = 69380.144| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.66 r_work: 0.2771 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35526 Z= 0.096 Angle : 0.539 11.564 48060 Z= 0.256 Chirality : 0.043 0.139 5436 Planarity : 0.003 0.038 6288 Dihedral : 6.432 56.826 5022 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.68 % Allowed : 21.35 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4398 helix: 1.27 (0.13), residues: 1764 sheet: -0.32 (0.26), residues: 396 loop : -1.20 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 225 TYR 0.007 0.001 TYR C 138 PHE 0.016 0.001 PHE C 742 TRP 0.043 0.003 TRP C 551 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00224 (35526) covalent geometry : angle 0.53903 (48060) hydrogen bonds : bond 0.02631 ( 1264) hydrogen bonds : angle 3.71932 ( 3546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (tm) REVERT: A 158 MET cc_start: 0.5192 (pmm) cc_final: 0.4915 (pmm) REVERT: A 163 PHE cc_start: 0.7076 (t80) cc_final: 0.6305 (t80) REVERT: B 158 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.4924 (pmm) REVERT: B 163 PHE cc_start: 0.6894 (t80) cc_final: 0.6388 (t80) REVERT: B 561 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: B 758 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.7435 (t80) REVERT: C 158 MET cc_start: 0.5115 (pmm) cc_final: 0.4550 (pmm) REVERT: C 758 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.7412 (t80) REVERT: D 59 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8237 (tm) REVERT: D 158 MET cc_start: 0.4737 (pmm) cc_final: 0.4374 (pmm) REVERT: D 163 PHE cc_start: 0.6913 (t80) cc_final: 0.6706 (t80) REVERT: E 158 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5420 (ppp) REVERT: E 163 PHE cc_start: 0.6658 (t80) cc_final: 0.6348 (t80) REVERT: E 508 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: E 758 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7500 (t80) REVERT: F 158 MET cc_start: 0.5084 (pmm) cc_final: 0.4704 (pmm) REVERT: F 758 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7481 (t80) outliers start: 63 outliers final: 39 residues processed: 227 average time/residue: 0.6614 time to fit residues: 183.7904 Evaluate side-chains 225 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 758 PHE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 551 TRP Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 758 PHE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 133 optimal weight: 5.9990 chunk 365 optimal weight: 0.0010 chunk 142 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 416 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.121293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071515 restraints weight = 69367.895| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.97 r_work: 0.2666 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 35526 Z= 0.215 Angle : 0.613 12.255 48060 Z= 0.291 Chirality : 0.046 0.144 5436 Planarity : 0.003 0.039 6288 Dihedral : 6.691 53.977 5022 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.97 % Allowed : 21.11 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 4398 helix: 1.13 (0.13), residues: 1806 sheet: -0.27 (0.26), residues: 396 loop : -1.14 (0.14), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 191 TYR 0.008 0.001 TYR A 138 PHE 0.020 0.001 PHE A 742 TRP 0.051 0.005 TRP D 551 HIS 0.004 0.001 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00504 (35526) covalent geometry : angle 0.61262 (48060) hydrogen bonds : bond 0.03234 ( 1264) hydrogen bonds : angle 3.88055 ( 3546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 171 time to evaluate : 1.371 Fit side-chains REVERT: A 59 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8271 (tm) REVERT: A 158 MET cc_start: 0.5451 (pmm) cc_final: 0.5172 (pmm) REVERT: A 163 PHE cc_start: 0.6794 (t80) cc_final: 0.6207 (t80) REVERT: B 158 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5381 (ppp) REVERT: B 163 PHE cc_start: 0.6767 (t80) cc_final: 0.6251 (t80) REVERT: B 561 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: C 158 MET cc_start: 0.5141 (pmm) cc_final: 0.4583 (pmm) REVERT: C 758 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.7705 (t80) REVERT: D 59 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8303 (tm) REVERT: D 158 MET cc_start: 0.4916 (pmm) cc_final: 0.4550 (pmm) REVERT: E 158 MET cc_start: 0.5933 (OUTLIER) cc_final: 0.5564 (ppp) REVERT: F 158 MET cc_start: 0.5249 (pmm) cc_final: 0.4867 (pmm) REVERT: F 758 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.7660 (t80) outliers start: 74 outliers final: 46 residues processed: 229 average time/residue: 0.6699 time to fit residues: 187.8942 Evaluate side-chains 221 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 362 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 411 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 114 optimal weight: 0.0470 chunk 233 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 347 optimal weight: 0.9990 chunk 392 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.123415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.074413 restraints weight = 69215.549| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.72 r_work: 0.2736 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35526 Z= 0.101 Angle : 0.558 12.901 48060 Z= 0.264 Chirality : 0.043 0.139 5436 Planarity : 0.003 0.038 6288 Dihedral : 6.519 56.936 5022 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.62 % Allowed : 21.49 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 4398 helix: 1.33 (0.13), residues: 1764 sheet: -0.33 (0.26), residues: 396 loop : -1.09 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 560 TYR 0.006 0.001 TYR E 517 PHE 0.015 0.001 PHE F 742 TRP 0.055 0.004 TRP C 551 HIS 0.002 0.000 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00241 (35526) covalent geometry : angle 0.55791 (48060) hydrogen bonds : bond 0.02723 ( 1264) hydrogen bonds : angle 3.72168 ( 3546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8285 (tm) REVERT: A 158 MET cc_start: 0.5241 (pmm) cc_final: 0.4953 (pmm) REVERT: A 163 PHE cc_start: 0.6857 (t80) cc_final: 0.6165 (t80) REVERT: B 158 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.5203 (pmm) REVERT: B 163 PHE cc_start: 0.6766 (t80) cc_final: 0.6268 (t80) REVERT: B 561 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: C 158 MET cc_start: 0.5018 (pmm) cc_final: 0.4454 (pmm) REVERT: C 678 MET cc_start: 0.9195 (mmp) cc_final: 0.8982 (mmm) REVERT: C 758 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.7474 (t80) REVERT: D 59 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8355 (tm) REVERT: D 158 MET cc_start: 0.4926 (pmm) cc_final: 0.4635 (pmm) REVERT: D 163 PHE cc_start: 0.7035 (t80) cc_final: 0.6568 (t80) REVERT: E 84 MET cc_start: 0.3428 (mpp) cc_final: 0.3009 (tpp) REVERT: E 158 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5553 (ppp) REVERT: F 158 MET cc_start: 0.5216 (pmm) cc_final: 0.4835 (pmm) REVERT: F 758 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7466 (t80) outliers start: 61 outliers final: 40 residues processed: 223 average time/residue: 0.6709 time to fit residues: 183.1458 Evaluate side-chains 219 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain D residue 757 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 758 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 275 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 401 optimal weight: 0.4980 chunk 298 optimal weight: 2.9990 chunk 430 optimal weight: 0.7980 chunk 230 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 215 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.124150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075291 restraints weight = 69316.966| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.66 r_work: 0.2759 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35526 Z= 0.099 Angle : 0.560 13.192 48060 Z= 0.263 Chirality : 0.043 0.141 5436 Planarity : 0.003 0.039 6288 Dihedral : 6.377 56.223 5022 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.62 % Allowed : 21.49 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 4398 helix: 1.39 (0.13), residues: 1764 sheet: -0.30 (0.26), residues: 396 loop : -1.08 (0.14), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 560 TYR 0.006 0.001 TYR A 138 PHE 0.020 0.001 PHE A 742 TRP 0.055 0.004 TRP D 551 HIS 0.002 0.000 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00235 (35526) covalent geometry : angle 0.56008 (48060) hydrogen bonds : bond 0.02608 ( 1264) hydrogen bonds : angle 3.66928 ( 3546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10701.04 seconds wall clock time: 183 minutes 24.29 seconds (11004.29 seconds total)