Starting phenix.real_space_refine on Sat Aug 23 03:50:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcx_37113/08_2025/8kcx_37113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcx_37113/08_2025/8kcx_37113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kcx_37113/08_2025/8kcx_37113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcx_37113/08_2025/8kcx_37113.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kcx_37113/08_2025/8kcx_37113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcx_37113/08_2025/8kcx_37113.map" } resolution = 2.96 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 56 5.16 5 C 6264 2.51 5 N 1456 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9486 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4608 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 550} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4608 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 550} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.26 Number of scatterers: 9486 At special positions: 0 Unit cell: (95.865, 83.415, 128.235, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 56 16.00 O 1708 8.00 N 1456 7.00 C 6264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 782 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG E 1 " - " ASN A 83 " " NAG F 1 " - " ASN A 136 " " NAG G 1 " - " ASN A 67 " " NAG H 1 " - " ASN A 57 " " NAG I 1 " - " ASN C 83 " " NAG J 1 " - " ASN C 136 " " NAG K 1 " - " ASN C 67 " " NAG L 1 " - " ASN C 57 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 350.5 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 791 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 563 " pdb="ZN ZN C 901 " - pdb=" NE2 HIS C 795 " 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 48.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.869A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 473 removed outlier: 3.855A pdb=" N ILE A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.565A pdb=" N GLN A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.873A pdb=" N ALA A 486 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.774A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.845A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 563 removed outlier: 3.558A pdb=" N GLY A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 575 removed outlier: 3.540A pdb=" N PHE A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 575' Processing helix chain 'A' and resid 575 through 592 Processing helix chain 'A' and resid 606 through 615 removed outlier: 3.592A pdb=" N VAL A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.801A pdb=" N VAL A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.741A pdb=" N SER A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.572A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 735 removed outlier: 4.131A pdb=" N LEU A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 723 " --> pdb=" O CYS A 719 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 762 removed outlier: 3.558A pdb=" N CYS A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 789 through 811 removed outlier: 3.630A pdb=" N ALA A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 302 through 335 removed outlier: 3.869A pdb=" N TYR C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE C 317 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS C 331 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 335 " --> pdb=" O HIS C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 473 removed outlier: 3.855A pdb=" N ILE C 449 " --> pdb=" O PHE C 445 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 450 " --> pdb=" O TRP C 446 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C 452 " --> pdb=" O ILE C 448 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.565A pdb=" N GLN C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.873A pdb=" N ALA C 486 " --> pdb=" O PHE C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 500 removed outlier: 3.774A pdb=" N ILE C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.845A pdb=" N GLY C 508 " --> pdb=" O HIS C 504 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 563 removed outlier: 3.558A pdb=" N GLY C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 575 removed outlier: 3.540A pdb=" N PHE C 571 " --> pdb=" O ASN C 567 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 572 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 574 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 575 " --> pdb=" O PHE C 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 575' Processing helix chain 'C' and resid 575 through 592 Processing helix chain 'C' and resid 606 through 615 removed outlier: 3.592A pdb=" N VAL C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 removed outlier: 3.801A pdb=" N VAL C 620 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.741A pdb=" N SER C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 649 removed outlier: 3.572A pdb=" N SER C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 645 " --> pdb=" O LEU C 641 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 647 " --> pdb=" O LEU C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 735 removed outlier: 4.131A pdb=" N LEU C 721 " --> pdb=" O PHE C 717 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 723 " --> pdb=" O CYS C 719 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 729 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 730 " --> pdb=" O ALA C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 762 removed outlier: 3.558A pdb=" N CYS C 746 " --> pdb=" O VAL C 742 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 760 " --> pdb=" O ALA C 756 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 776 Processing helix chain 'C' and resid 777 through 779 No H-bonds generated for 'chain 'C' and resid 777 through 779' Processing helix chain 'C' and resid 789 through 811 removed outlier: 3.630A pdb=" N ALA C 799 " --> pdb=" O HIS C 795 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 4.809A pdb=" N ASN A 67 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.456A pdb=" N ALA A 77 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.856A pdb=" N ARG A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 4.809A pdb=" N ASN C 67 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 56 removed outlier: 4.456A pdb=" N ALA C 77 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.856A pdb=" N ARG C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 192 488 hydrogen bonds defined for protein. 1398 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: 1.48 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2794 1.34 - 1.46: 2618 1.46 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 9732 Sorted by residual: bond pdb=" N ILE A 581 " pdb=" CA ILE A 581 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE C 581 " pdb=" CA ILE C 581 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" N ILE A 612 " pdb=" CA ILE A 612 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" N ILE C 612 " pdb=" CA ILE C 612 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" N MET A 152 " pdb=" CA MET A 152 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.03e+00 ... (remaining 9727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12800 2.02 - 4.05: 386 4.05 - 6.07: 34 6.07 - 8.10: 6 8.10 - 10.12: 10 Bond angle restraints: 13236 Sorted by residual: angle pdb=" N LEU A 516 " pdb=" CA LEU A 516 " pdb=" C LEU A 516 " ideal model delta sigma weight residual 111.36 107.64 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N LEU C 516 " pdb=" CA LEU C 516 " pdb=" C LEU C 516 " ideal model delta sigma weight residual 111.36 107.64 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" N THR C 575 " pdb=" CA THR C 575 " pdb=" C THR C 575 " ideal model delta sigma weight residual 113.12 109.07 4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N THR A 575 " pdb=" CA THR A 575 " pdb=" C THR A 575 " ideal model delta sigma weight residual 113.12 109.07 4.05 1.25e+00 6.40e-01 1.05e+01 angle pdb=" N ILE C 451 " pdb=" CA ILE C 451 " pdb=" C ILE C 451 " ideal model delta sigma weight residual 110.72 107.46 3.26 1.01e+00 9.80e-01 1.04e+01 ... (remaining 13231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 5264 21.51 - 43.02: 484 43.02 - 64.52: 74 64.52 - 86.03: 40 86.03 - 107.54: 48 Dihedral angle restraints: 5910 sinusoidal: 2520 harmonic: 3390 Sorted by residual: dihedral pdb=" CB CYS A 212 " pdb=" SG CYS A 212 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual 93.00 54.10 38.90 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" CB CYS C 212 " pdb=" SG CYS C 212 " pdb=" SG CYS C 271 " pdb=" CB CYS C 271 " ideal model delta sinusoidal sigma weight residual 93.00 54.10 38.90 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" CB CYS C 485 " pdb=" SG CYS C 485 " pdb=" SG CYS C 782 " pdb=" CB CYS C 782 " ideal model delta sinusoidal sigma weight residual 93.00 126.23 -33.23 1 1.00e+01 1.00e-02 1.57e+01 ... (remaining 5907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1228 0.057 - 0.114: 264 0.114 - 0.172: 64 0.172 - 0.229: 12 0.229 - 0.286: 6 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1571 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 182 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 183 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 182 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 183 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 771 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 772 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 772 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 772 " -0.022 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2659 2.80 - 3.32: 7823 3.32 - 3.85: 15509 3.85 - 4.37: 17476 4.37 - 4.90: 30672 Nonbonded interactions: 74139 Sorted by model distance: nonbonded pdb=" OG SER A 59 " pdb=" O3 NAG H 1 " model vdw 2.273 3.040 nonbonded pdb=" OG SER C 59 " pdb=" O3 NAG L 1 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASN A 447 " pdb=" CD1 LEU C 587 " model vdw 2.292 3.460 nonbonded pdb=" CD1 LEU A 587 " pdb=" OD1 ASN C 447 " model vdw 2.292 3.460 nonbonded pdb=" OH TYR C 210 " pdb=" O GLY C 272 " model vdw 2.294 3.040 ... (remaining 74134 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } 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: 0.560 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 9766 Z= 0.297 Angle : 0.785 10.121 13312 Z= 0.436 Chirality : 0.055 0.286 1574 Planarity : 0.004 0.050 1604 Dihedral : 20.462 107.539 3694 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.39 % Allowed : 19.02 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.22), residues: 1114 helix: -3.03 (0.15), residues: 498 sheet: 1.43 (0.30), residues: 270 loop : -1.68 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.016 0.001 TYR C 724 PHE 0.012 0.001 PHE C 454 TRP 0.009 0.001 TRP A 106 HIS 0.007 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 9732) covalent geometry : angle 0.76920 (13236) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.78465 ( 16) hydrogen bonds : bond 0.26077 ( 488) hydrogen bonds : angle 8.60234 ( 1398) metal coordination : bond 0.09927 ( 6) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 1.45810 ( 36) link_NAG-ASN : bond 0.00424 ( 8) link_NAG-ASN : angle 3.40941 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LYS cc_start: 0.9196 (pttt) cc_final: 0.8989 (pttp) REVERT: A 256 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8336 (mp0) REVERT: A 265 LYS cc_start: 0.9253 (mttm) cc_final: 0.8920 (mtpt) REVERT: A 446 TRP cc_start: 0.8147 (t60) cc_final: 0.7544 (t-100) REVERT: A 451 ILE cc_start: 0.8639 (mt) cc_final: 0.8288 (mp) REVERT: A 550 ILE cc_start: 0.9272 (mm) cc_final: 0.9037 (mm) REVERT: A 713 MET cc_start: 0.9041 (tpp) cc_final: 0.8838 (tpt) REVERT: A 721 LEU cc_start: 0.8898 (tt) cc_final: 0.8515 (mt) REVERT: A 754 TRP cc_start: 0.9348 (m100) cc_final: 0.9077 (m100) REVERT: A 774 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8589 (mt-10) REVERT: C 251 LYS cc_start: 0.9196 (pttt) cc_final: 0.8990 (pttp) REVERT: C 256 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8336 (mp0) REVERT: C 265 LYS cc_start: 0.9256 (mttm) cc_final: 0.8922 (mtpt) REVERT: C 446 TRP cc_start: 0.8149 (t60) cc_final: 0.7544 (t-100) REVERT: C 451 ILE cc_start: 0.8639 (mt) cc_final: 0.8289 (mp) REVERT: C 550 ILE cc_start: 0.9271 (mm) cc_final: 0.9035 (mm) REVERT: C 713 MET cc_start: 0.9042 (tpp) cc_final: 0.8837 (tpt) REVERT: C 721 LEU cc_start: 0.8900 (tt) cc_final: 0.8516 (mt) REVERT: C 754 TRP cc_start: 0.9345 (m100) cc_final: 0.9075 (m100) REVERT: C 774 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8588 (mt-10) outliers start: 4 outliers final: 2 residues processed: 282 average time/residue: 0.4331 time to fit residues: 132.7784 Evaluate side-chains 212 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 TYR Chi-restraints excluded: chain C residue 579 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 501 ASN C 467 GLN C 501 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096546 restraints weight = 12463.765| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.81 r_work: 0.2938 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9766 Z= 0.141 Angle : 0.626 8.087 13312 Z= 0.304 Chirality : 0.044 0.264 1574 Planarity : 0.004 0.038 1604 Dihedral : 15.673 85.037 1644 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.82 % Allowed : 21.86 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.23), residues: 1114 helix: -0.70 (0.20), residues: 500 sheet: 1.31 (0.30), residues: 270 loop : -1.47 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 518 TYR 0.013 0.001 TYR C 188 PHE 0.010 0.001 PHE A 608 TRP 0.010 0.001 TRP A 106 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9732) covalent geometry : angle 0.61040 (13236) SS BOND : bond 0.00096 ( 8) SS BOND : angle 0.65764 ( 16) hydrogen bonds : bond 0.05317 ( 488) hydrogen bonds : angle 4.77590 ( 1398) metal coordination : bond 0.00492 ( 6) link_BETA1-4 : bond 0.00339 ( 12) link_BETA1-4 : angle 2.06485 ( 36) link_NAG-ASN : bond 0.00369 ( 8) link_NAG-ASN : angle 2.27494 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8475 (mp10) cc_final: 0.8187 (mm-40) REVERT: A 188 TYR cc_start: 0.9336 (p90) cc_final: 0.9121 (p90) REVERT: A 226 ASP cc_start: 0.9335 (p0) cc_final: 0.9119 (p0) REVERT: A 256 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8449 (mp0) REVERT: A 265 LYS cc_start: 0.9301 (mttm) cc_final: 0.9002 (mtpt) REVERT: A 334 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.5928 (tpm170) REVERT: A 446 TRP cc_start: 0.8062 (OUTLIER) cc_final: 0.7530 (t-100) REVERT: A 546 TYR cc_start: 0.8423 (m-10) cc_final: 0.8189 (m-10) REVERT: A 554 MET cc_start: 0.8599 (tpp) cc_final: 0.8101 (tpp) REVERT: A 559 SER cc_start: 0.8938 (m) cc_final: 0.8624 (t) REVERT: A 713 MET cc_start: 0.8922 (tpp) cc_final: 0.8711 (tpt) REVERT: A 754 TRP cc_start: 0.9185 (m100) cc_final: 0.8860 (m100) REVERT: A 774 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8741 (mt-10) REVERT: C 123 GLN cc_start: 0.8460 (mp10) cc_final: 0.8174 (mm-40) REVERT: C 188 TYR cc_start: 0.9335 (p90) cc_final: 0.9114 (p90) REVERT: C 226 ASP cc_start: 0.9335 (p0) cc_final: 0.9113 (p0) REVERT: C 256 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8425 (mp0) REVERT: C 265 LYS cc_start: 0.9304 (mttm) cc_final: 0.9007 (mtpt) REVERT: C 334 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.5930 (tpm170) REVERT: C 446 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7530 (t-100) REVERT: C 546 TYR cc_start: 0.8419 (m-10) cc_final: 0.8183 (m-10) REVERT: C 554 MET cc_start: 0.8603 (tpp) cc_final: 0.8105 (tpp) REVERT: C 559 SER cc_start: 0.8934 (m) cc_final: 0.8620 (t) REVERT: C 713 MET cc_start: 0.8924 (tpp) cc_final: 0.8712 (tpt) REVERT: C 754 TRP cc_start: 0.9175 (m100) cc_final: 0.8850 (m100) REVERT: C 774 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8745 (mt-10) outliers start: 39 outliers final: 16 residues processed: 256 average time/residue: 0.3980 time to fit residues: 111.9239 Evaluate side-chains 240 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN A 570 ASN C 475 ASN C 570 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095367 restraints weight = 12481.239| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.86 r_work: 0.2924 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9766 Z= 0.145 Angle : 0.601 8.272 13312 Z= 0.284 Chirality : 0.045 0.277 1574 Planarity : 0.003 0.034 1604 Dihedral : 10.964 70.586 1640 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.71 % Allowed : 22.35 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.23), residues: 1114 helix: 0.52 (0.23), residues: 488 sheet: 1.25 (0.29), residues: 270 loop : -1.38 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 518 TYR 0.015 0.001 TYR A 568 PHE 0.020 0.001 PHE A 312 TRP 0.010 0.001 TRP C 106 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9732) covalent geometry : angle 0.58548 (13236) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.62859 ( 16) hydrogen bonds : bond 0.04387 ( 488) hydrogen bonds : angle 4.23814 ( 1398) metal coordination : bond 0.00409 ( 6) link_BETA1-4 : bond 0.00493 ( 12) link_BETA1-4 : angle 2.09586 ( 36) link_NAG-ASN : bond 0.00373 ( 8) link_NAG-ASN : angle 2.13156 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8580 (mp10) cc_final: 0.8329 (mm-40) REVERT: A 256 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8450 (mp0) REVERT: A 265 LYS cc_start: 0.9346 (mttm) cc_final: 0.9041 (mtpt) REVERT: A 302 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7997 (mmmt) REVERT: A 334 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.5972 (tpm170) REVERT: A 446 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7570 (t-100) REVERT: A 554 MET cc_start: 0.8690 (tpp) cc_final: 0.8288 (tpp) REVERT: A 559 SER cc_start: 0.8937 (m) cc_final: 0.8671 (t) REVERT: A 713 MET cc_start: 0.8864 (tpp) cc_final: 0.8584 (tpt) REVERT: A 737 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 774 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8798 (mt-10) REVERT: C 123 GLN cc_start: 0.8575 (mp10) cc_final: 0.8325 (mm-40) REVERT: C 256 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8445 (mp0) REVERT: C 265 LYS cc_start: 0.9344 (mttm) cc_final: 0.9040 (mtpt) REVERT: C 302 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7983 (mmmt) REVERT: C 334 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.5977 (tpm170) REVERT: C 446 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7570 (t-100) REVERT: C 554 MET cc_start: 0.8689 (tpp) cc_final: 0.8286 (tpp) REVERT: C 559 SER cc_start: 0.8933 (m) cc_final: 0.8667 (t) REVERT: C 713 MET cc_start: 0.8867 (tpp) cc_final: 0.8581 (tpt) REVERT: C 737 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: C 774 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8795 (mt-10) outliers start: 48 outliers final: 27 residues processed: 263 average time/residue: 0.3693 time to fit residues: 106.0102 Evaluate side-chains 257 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 467 GLN A 572 GLN C 121 ASN C 467 GLN C 572 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.096063 restraints weight = 12447.875| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.88 r_work: 0.2935 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9766 Z= 0.119 Angle : 0.553 9.149 13312 Z= 0.263 Chirality : 0.044 0.265 1574 Planarity : 0.003 0.033 1604 Dihedral : 8.029 55.985 1640 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 5.49 % Allowed : 22.35 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.24), residues: 1114 helix: 1.01 (0.23), residues: 488 sheet: 1.28 (0.29), residues: 270 loop : -1.23 (0.28), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.010 0.001 TYR C 188 PHE 0.008 0.001 PHE C 573 TRP 0.009 0.001 TRP C 106 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9732) covalent geometry : angle 0.53530 (13236) SS BOND : bond 0.00113 ( 8) SS BOND : angle 0.58651 ( 16) hydrogen bonds : bond 0.03779 ( 488) hydrogen bonds : angle 3.97063 ( 1398) metal coordination : bond 0.00243 ( 6) link_BETA1-4 : bond 0.00502 ( 12) link_BETA1-4 : angle 2.25464 ( 36) link_NAG-ASN : bond 0.00353 ( 8) link_NAG-ASN : angle 1.93028 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.8990 (tt0) cc_final: 0.8752 (pm20) REVERT: A 256 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8413 (mp0) REVERT: A 265 LYS cc_start: 0.9349 (mttm) cc_final: 0.9021 (mtpt) REVERT: A 306 TYR cc_start: 0.9154 (m-80) cc_final: 0.8921 (m-80) REVERT: A 446 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7544 (t-100) REVERT: A 555 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 559 SER cc_start: 0.8899 (m) cc_final: 0.8641 (t) REVERT: A 568 TYR cc_start: 0.9100 (t80) cc_final: 0.8860 (t80) REVERT: A 572 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: A 578 MET cc_start: 0.7543 (mmp) cc_final: 0.7137 (mmm) REVERT: A 713 MET cc_start: 0.8836 (tpp) cc_final: 0.8557 (tpt) REVERT: A 774 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8795 (mt-10) REVERT: C 207 GLU cc_start: 0.8990 (tt0) cc_final: 0.8753 (pm20) REVERT: C 256 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8405 (mp0) REVERT: C 265 LYS cc_start: 0.9347 (mttm) cc_final: 0.9030 (mtpt) REVERT: C 306 TYR cc_start: 0.9154 (m-80) cc_final: 0.8920 (m-80) REVERT: C 446 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7544 (t-100) REVERT: C 555 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 559 SER cc_start: 0.8902 (m) cc_final: 0.8643 (t) REVERT: C 568 TYR cc_start: 0.9103 (t80) cc_final: 0.8866 (t80) REVERT: C 572 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: C 578 MET cc_start: 0.7541 (mmp) cc_final: 0.7138 (mmm) REVERT: C 713 MET cc_start: 0.8839 (tpp) cc_final: 0.8556 (tpt) REVERT: C 774 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8796 (mt-10) outliers start: 56 outliers final: 21 residues processed: 258 average time/residue: 0.3553 time to fit residues: 100.8604 Evaluate side-chains 250 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.094828 restraints weight = 12557.117| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.26 r_work: 0.2884 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9766 Z= 0.227 Angle : 0.608 8.934 13312 Z= 0.293 Chirality : 0.046 0.274 1574 Planarity : 0.003 0.036 1604 Dihedral : 7.318 58.692 1640 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 6.86 % Allowed : 23.33 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.24), residues: 1114 helix: 1.25 (0.23), residues: 488 sheet: 1.25 (0.29), residues: 270 loop : -1.20 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 523 TYR 0.013 0.001 TYR A 188 PHE 0.013 0.001 PHE C 509 TRP 0.009 0.001 TRP A 106 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 9732) covalent geometry : angle 0.59267 (13236) SS BOND : bond 0.00167 ( 8) SS BOND : angle 0.63019 ( 16) hydrogen bonds : bond 0.03947 ( 488) hydrogen bonds : angle 4.02725 ( 1398) metal coordination : bond 0.00633 ( 6) link_BETA1-4 : bond 0.00510 ( 12) link_BETA1-4 : angle 2.25071 ( 36) link_NAG-ASN : bond 0.00278 ( 8) link_NAG-ASN : angle 1.84276 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8423 (mp0) REVERT: A 265 LYS cc_start: 0.9373 (mttm) cc_final: 0.9064 (mtpt) REVERT: A 302 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7963 (mmtt) REVERT: A 306 TYR cc_start: 0.9203 (m-80) cc_final: 0.8923 (m-80) REVERT: A 334 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5617 (tpm170) REVERT: A 446 TRP cc_start: 0.8096 (OUTLIER) cc_final: 0.7597 (t-100) REVERT: A 542 PHE cc_start: 0.8066 (m-10) cc_final: 0.7742 (m-10) REVERT: A 554 MET cc_start: 0.8646 (tpp) cc_final: 0.8291 (tpp) REVERT: A 555 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 559 SER cc_start: 0.8986 (m) cc_final: 0.8736 (t) REVERT: A 578 MET cc_start: 0.7518 (mmp) cc_final: 0.7093 (mmm) REVERT: A 608 PHE cc_start: 0.4907 (OUTLIER) cc_final: 0.3574 (m-80) REVERT: A 713 MET cc_start: 0.8866 (tpp) cc_final: 0.8568 (tpt) REVERT: A 718 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 732 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8161 (tppp) REVERT: A 737 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: A 774 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8896 (mt-10) REVERT: A 790 ASP cc_start: 0.8917 (m-30) cc_final: 0.8538 (m-30) REVERT: C 256 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8414 (mp0) REVERT: C 265 LYS cc_start: 0.9368 (mttm) cc_final: 0.9060 (mtpt) REVERT: C 302 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7954 (mmtt) REVERT: C 306 TYR cc_start: 0.9202 (m-80) cc_final: 0.8923 (m-80) REVERT: C 334 ARG cc_start: 0.6152 (OUTLIER) cc_final: 0.5617 (tpm170) REVERT: C 446 TRP cc_start: 0.8096 (OUTLIER) cc_final: 0.7595 (t-100) REVERT: C 542 PHE cc_start: 0.8062 (m-10) cc_final: 0.7732 (m-10) REVERT: C 554 MET cc_start: 0.8653 (tpp) cc_final: 0.8296 (tpp) REVERT: C 555 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 559 SER cc_start: 0.8987 (m) cc_final: 0.8738 (t) REVERT: C 578 MET cc_start: 0.7523 (mmp) cc_final: 0.7101 (mmm) REVERT: C 608 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.3572 (m-80) REVERT: C 713 MET cc_start: 0.8870 (tpp) cc_final: 0.8571 (tpt) REVERT: C 718 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (mp) REVERT: C 732 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8156 (tppp) REVERT: C 737 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: C 774 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8902 (mt-10) REVERT: C 790 ASP cc_start: 0.8922 (m-30) cc_final: 0.8544 (m-30) outliers start: 70 outliers final: 36 residues processed: 258 average time/residue: 0.3923 time to fit residues: 111.2247 Evaluate side-chains 256 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN C 467 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097477 restraints weight = 12395.717| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.52 r_work: 0.2904 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9766 Z= 0.110 Angle : 0.543 8.953 13312 Z= 0.260 Chirality : 0.043 0.255 1574 Planarity : 0.003 0.033 1604 Dihedral : 6.278 50.513 1640 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.90 % Allowed : 24.41 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.24), residues: 1114 helix: 1.55 (0.23), residues: 490 sheet: 1.33 (0.29), residues: 270 loop : -1.12 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 523 TYR 0.020 0.001 TYR C 568 PHE 0.012 0.001 PHE C 573 TRP 0.008 0.001 TRP A 106 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9732) covalent geometry : angle 0.52826 (13236) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.63139 ( 16) hydrogen bonds : bond 0.03488 ( 488) hydrogen bonds : angle 3.81113 ( 1398) metal coordination : bond 0.00235 ( 6) link_BETA1-4 : bond 0.00498 ( 12) link_BETA1-4 : angle 2.05114 ( 36) link_NAG-ASN : bond 0.00353 ( 8) link_NAG-ASN : angle 1.79745 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8519 (mp0) REVERT: A 265 LYS cc_start: 0.9379 (mttm) cc_final: 0.9081 (mtpt) REVERT: A 302 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7957 (mmtt) REVERT: A 306 TYR cc_start: 0.9128 (m-80) cc_final: 0.8798 (m-80) REVERT: A 446 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.7641 (t-100) REVERT: A 542 PHE cc_start: 0.8030 (m-10) cc_final: 0.7675 (m-10) REVERT: A 555 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 559 SER cc_start: 0.8928 (m) cc_final: 0.8712 (t) REVERT: A 608 PHE cc_start: 0.4856 (OUTLIER) cc_final: 0.3613 (m-80) REVERT: A 713 MET cc_start: 0.8831 (tpp) cc_final: 0.8559 (tpt) REVERT: A 732 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (tppp) REVERT: A 774 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8864 (mt-10) REVERT: C 256 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8516 (mp0) REVERT: C 265 LYS cc_start: 0.9383 (mttm) cc_final: 0.9086 (mtpt) REVERT: C 302 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7950 (mmtt) REVERT: C 306 TYR cc_start: 0.9132 (m-80) cc_final: 0.8804 (m-80) REVERT: C 446 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.7641 (t-100) REVERT: C 542 PHE cc_start: 0.8025 (m-10) cc_final: 0.7665 (m-10) REVERT: C 555 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 559 SER cc_start: 0.8930 (m) cc_final: 0.8716 (t) REVERT: C 608 PHE cc_start: 0.4859 (OUTLIER) cc_final: 0.3613 (m-80) REVERT: C 713 MET cc_start: 0.8833 (tpp) cc_final: 0.8560 (tpt) REVERT: C 732 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8276 (tppp) REVERT: C 774 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8876 (mt-10) outliers start: 50 outliers final: 15 residues processed: 258 average time/residue: 0.4194 time to fit residues: 118.6396 Evaluate side-chains 243 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 0.0010 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 467 GLN C 467 GLN C 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096125 restraints weight = 12320.355| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.39 r_work: 0.2905 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9766 Z= 0.146 Angle : 0.553 9.202 13312 Z= 0.268 Chirality : 0.044 0.260 1574 Planarity : 0.003 0.034 1604 Dihedral : 5.622 50.420 1640 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 5.39 % Allowed : 23.92 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.24), residues: 1114 helix: 1.75 (0.23), residues: 490 sheet: 1.33 (0.29), residues: 270 loop : -1.09 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 523 TYR 0.012 0.001 TYR A 188 PHE 0.011 0.001 PHE A 509 TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9732) covalent geometry : angle 0.54088 (13236) SS BOND : bond 0.00121 ( 8) SS BOND : angle 0.59157 ( 16) hydrogen bonds : bond 0.03568 ( 488) hydrogen bonds : angle 3.78693 ( 1398) metal coordination : bond 0.00344 ( 6) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.88348 ( 36) link_NAG-ASN : bond 0.00270 ( 8) link_NAG-ASN : angle 1.72714 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8494 (mp0) REVERT: A 265 LYS cc_start: 0.9365 (mttm) cc_final: 0.9035 (mtpt) REVERT: A 302 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7980 (mmtt) REVERT: A 306 TYR cc_start: 0.9134 (m-80) cc_final: 0.8824 (m-80) REVERT: A 334 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5537 (tpm170) REVERT: A 446 TRP cc_start: 0.8003 (OUTLIER) cc_final: 0.7595 (t-100) REVERT: A 542 PHE cc_start: 0.8027 (m-10) cc_final: 0.7680 (m-10) REVERT: A 555 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 559 SER cc_start: 0.8886 (m) cc_final: 0.8672 (t) REVERT: A 608 PHE cc_start: 0.4924 (OUTLIER) cc_final: 0.3707 (m-80) REVERT: A 713 MET cc_start: 0.8793 (tpp) cc_final: 0.8551 (tpt) REVERT: A 732 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8269 (tppp) REVERT: A 774 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8824 (mt-10) REVERT: C 256 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8482 (mp0) REVERT: C 265 LYS cc_start: 0.9367 (mttm) cc_final: 0.9040 (mtpt) REVERT: C 302 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7977 (mmtt) REVERT: C 306 TYR cc_start: 0.9133 (m-80) cc_final: 0.8824 (m-80) REVERT: C 334 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5538 (tpm170) REVERT: C 446 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.7594 (t-100) REVERT: C 542 PHE cc_start: 0.8019 (m-10) cc_final: 0.7672 (m-10) REVERT: C 555 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 559 SER cc_start: 0.8891 (m) cc_final: 0.8677 (t) REVERT: C 572 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: C 608 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.3698 (m-80) REVERT: C 713 MET cc_start: 0.8798 (tpp) cc_final: 0.8552 (tpt) REVERT: C 732 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8263 (tppp) REVERT: C 774 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8842 (mt-10) outliers start: 55 outliers final: 26 residues processed: 263 average time/residue: 0.4534 time to fit residues: 129.9274 Evaluate side-chains 245 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 572 GLN A 764 ASN C 467 GLN C 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093251 restraints weight = 12411.093| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.87 r_work: 0.2896 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9766 Z= 0.241 Angle : 0.621 9.405 13312 Z= 0.307 Chirality : 0.047 0.266 1574 Planarity : 0.003 0.039 1604 Dihedral : 5.562 50.171 1640 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.10 % Allowed : 24.90 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.24), residues: 1114 helix: 1.77 (0.23), residues: 490 sheet: 1.25 (0.29), residues: 270 loop : -1.10 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 523 TYR 0.025 0.001 TYR C 568 PHE 0.013 0.001 PHE C 573 TRP 0.009 0.001 TRP C 106 HIS 0.004 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 9732) covalent geometry : angle 0.61121 (13236) SS BOND : bond 0.00173 ( 8) SS BOND : angle 0.68602 ( 16) hydrogen bonds : bond 0.03805 ( 488) hydrogen bonds : angle 3.90848 ( 1398) metal coordination : bond 0.00627 ( 6) link_BETA1-4 : bond 0.00468 ( 12) link_BETA1-4 : angle 1.78368 ( 36) link_NAG-ASN : bond 0.00255 ( 8) link_NAG-ASN : angle 1.75140 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8428 (mp0) REVERT: A 265 LYS cc_start: 0.9384 (mttm) cc_final: 0.9069 (mtpt) REVERT: A 302 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7990 (mmtt) REVERT: A 306 TYR cc_start: 0.9184 (m-80) cc_final: 0.8832 (m-80) REVERT: A 334 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5562 (tpm170) REVERT: A 446 TRP cc_start: 0.8066 (OUTLIER) cc_final: 0.7657 (t-100) REVERT: A 554 MET cc_start: 0.8617 (tpp) cc_final: 0.8227 (tpp) REVERT: A 555 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 559 SER cc_start: 0.8940 (m) cc_final: 0.8721 (t) REVERT: A 567 ASN cc_start: 0.8560 (t0) cc_final: 0.8126 (t0) REVERT: A 572 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: A 578 MET cc_start: 0.7568 (mmp) cc_final: 0.7148 (mmm) REVERT: A 608 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3585 (m-80) REVERT: A 713 MET cc_start: 0.8850 (tpp) cc_final: 0.8572 (tpt) REVERT: A 728 TYR cc_start: 0.7014 (m-80) cc_final: 0.6739 (m-80) REVERT: A 732 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8226 (tppp) REVERT: A 737 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: A 774 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8849 (mt-10) REVERT: A 790 ASP cc_start: 0.8895 (m-30) cc_final: 0.8529 (m-30) REVERT: C 256 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8415 (mp0) REVERT: C 265 LYS cc_start: 0.9381 (mttm) cc_final: 0.9069 (mtpt) REVERT: C 302 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7975 (mmtt) REVERT: C 306 TYR cc_start: 0.9187 (m-80) cc_final: 0.8837 (m-80) REVERT: C 334 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5560 (tpm170) REVERT: C 446 TRP cc_start: 0.8066 (OUTLIER) cc_final: 0.7655 (t-100) REVERT: C 554 MET cc_start: 0.8619 (tpp) cc_final: 0.8228 (tpp) REVERT: C 555 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 559 SER cc_start: 0.8941 (m) cc_final: 0.8723 (t) REVERT: C 567 ASN cc_start: 0.8549 (t0) cc_final: 0.8112 (t0) REVERT: C 578 MET cc_start: 0.7558 (mmp) cc_final: 0.7141 (mmm) REVERT: C 608 PHE cc_start: 0.4953 (OUTLIER) cc_final: 0.3573 (m-80) REVERT: C 713 MET cc_start: 0.8855 (tpp) cc_final: 0.8571 (tpt) REVERT: C 728 TYR cc_start: 0.7005 (m-80) cc_final: 0.6728 (m-80) REVERT: C 732 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8213 (tppp) REVERT: C 737 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: C 774 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8870 (mt-10) REVERT: C 790 ASP cc_start: 0.8892 (m-30) cc_final: 0.8524 (m-30) outliers start: 52 outliers final: 33 residues processed: 242 average time/residue: 0.4173 time to fit residues: 111.3371 Evaluate side-chains 255 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 221 MET Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 764 ASN C 467 GLN C 572 GLN C 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092870 restraints weight = 12587.759| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.89 r_work: 0.2886 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9766 Z= 0.194 Angle : 0.605 9.534 13312 Z= 0.298 Chirality : 0.046 0.262 1574 Planarity : 0.003 0.039 1604 Dihedral : 5.476 50.239 1640 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.80 % Allowed : 25.00 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.24), residues: 1114 helix: 1.82 (0.23), residues: 490 sheet: 1.25 (0.29), residues: 270 loop : -1.11 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 523 TYR 0.014 0.001 TYR C 188 PHE 0.012 0.001 PHE C 573 TRP 0.009 0.001 TRP A 106 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9732) covalent geometry : angle 0.59426 (13236) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.66214 ( 16) hydrogen bonds : bond 0.03735 ( 488) hydrogen bonds : angle 3.87961 ( 1398) metal coordination : bond 0.00463 ( 6) link_BETA1-4 : bond 0.00450 ( 12) link_BETA1-4 : angle 1.75172 ( 36) link_NAG-ASN : bond 0.00276 ( 8) link_NAG-ASN : angle 1.78816 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7896 (p0) REVERT: A 124 GLU cc_start: 0.8715 (mp0) cc_final: 0.7853 (tp30) REVERT: A 256 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8359 (mp0) REVERT: A 265 LYS cc_start: 0.9376 (mttm) cc_final: 0.9057 (mtpt) REVERT: A 302 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: A 306 TYR cc_start: 0.9104 (m-80) cc_final: 0.8732 (m-80) REVERT: A 334 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5588 (tpm170) REVERT: A 446 TRP cc_start: 0.8049 (OUTLIER) cc_final: 0.7666 (t-100) REVERT: A 554 MET cc_start: 0.8610 (tpp) cc_final: 0.8224 (tpp) REVERT: A 555 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 559 SER cc_start: 0.8899 (m) cc_final: 0.8675 (t) REVERT: A 567 ASN cc_start: 0.8544 (t0) cc_final: 0.8128 (t0) REVERT: A 572 GLN cc_start: 0.8813 (mp10) cc_final: 0.8444 (mp10) REVERT: A 578 MET cc_start: 0.7582 (mmp) cc_final: 0.7154 (mmm) REVERT: A 608 PHE cc_start: 0.4991 (OUTLIER) cc_final: 0.3646 (m-80) REVERT: A 713 MET cc_start: 0.8851 (tpp) cc_final: 0.8570 (tpt) REVERT: A 732 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8193 (tppp) REVERT: A 737 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: A 774 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8811 (mt-10) REVERT: A 792 ASP cc_start: 0.8852 (m-30) cc_final: 0.8632 (m-30) REVERT: C 73 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7889 (p0) REVERT: C 124 GLU cc_start: 0.8720 (mp0) cc_final: 0.7864 (tp30) REVERT: C 256 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8346 (mp0) REVERT: C 265 LYS cc_start: 0.9376 (mttm) cc_final: 0.9057 (mtpt) REVERT: C 302 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7865 (mmtt) REVERT: C 306 TYR cc_start: 0.9103 (m-80) cc_final: 0.8729 (m-80) REVERT: C 334 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5581 (tpm170) REVERT: C 446 TRP cc_start: 0.8048 (OUTLIER) cc_final: 0.7666 (t-100) REVERT: C 554 MET cc_start: 0.8622 (tpp) cc_final: 0.8232 (tpp) REVERT: C 555 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 559 SER cc_start: 0.8907 (m) cc_final: 0.8683 (t) REVERT: C 567 ASN cc_start: 0.8589 (t0) cc_final: 0.8167 (t0) REVERT: C 572 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8627 (mp10) REVERT: C 578 MET cc_start: 0.7583 (mmp) cc_final: 0.7157 (mmm) REVERT: C 608 PHE cc_start: 0.4992 (OUTLIER) cc_final: 0.3647 (m-80) REVERT: C 713 MET cc_start: 0.8852 (tpp) cc_final: 0.8571 (tpt) REVERT: C 732 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8191 (tppp) REVERT: C 737 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: C 774 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8834 (mt-10) REVERT: C 792 ASP cc_start: 0.8853 (m-30) cc_final: 0.8633 (m-30) outliers start: 49 outliers final: 28 residues processed: 239 average time/residue: 0.4126 time to fit residues: 108.6113 Evaluate side-chains 247 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 572 GLN C 467 GLN C 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095009 restraints weight = 12480.079| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.87 r_work: 0.2914 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9766 Z= 0.113 Angle : 0.584 9.739 13312 Z= 0.284 Chirality : 0.044 0.251 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.323 50.738 1640 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.71 % Allowed : 25.29 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.24), residues: 1114 helix: 1.93 (0.23), residues: 490 sheet: 1.34 (0.29), residues: 270 loop : -1.08 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 523 TYR 0.024 0.001 TYR C 568 PHE 0.009 0.001 PHE C 573 TRP 0.008 0.001 TRP A 106 HIS 0.002 0.001 HIS A 791 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9732) covalent geometry : angle 0.57285 (13236) SS BOND : bond 0.00116 ( 8) SS BOND : angle 0.61445 ( 16) hydrogen bonds : bond 0.03488 ( 488) hydrogen bonds : angle 3.78151 ( 1398) metal coordination : bond 0.00126 ( 6) link_BETA1-4 : bond 0.00447 ( 12) link_BETA1-4 : angle 1.72471 ( 36) link_NAG-ASN : bond 0.00333 ( 8) link_NAG-ASN : angle 1.83284 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7898 (p0) REVERT: A 256 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8361 (mp0) REVERT: A 265 LYS cc_start: 0.9356 (mttm) cc_final: 0.9033 (mtpt) REVERT: A 302 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7802 (mmtt) REVERT: A 306 TYR cc_start: 0.9043 (m-80) cc_final: 0.8685 (m-80) REVERT: A 334 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5570 (tpm170) REVERT: A 446 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.7666 (t-100) REVERT: A 554 MET cc_start: 0.8565 (tpp) cc_final: 0.8177 (tpp) REVERT: A 555 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 559 SER cc_start: 0.8880 (m) cc_final: 0.8671 (t) REVERT: A 567 ASN cc_start: 0.8537 (t0) cc_final: 0.8085 (t0) REVERT: A 572 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: A 578 MET cc_start: 0.7543 (mmp) cc_final: 0.7092 (mmm) REVERT: A 608 PHE cc_start: 0.4967 (OUTLIER) cc_final: 0.3637 (m-80) REVERT: A 713 MET cc_start: 0.8839 (tpp) cc_final: 0.8565 (tpt) REVERT: A 732 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (tppt) REVERT: A 737 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 774 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 792 ASP cc_start: 0.8825 (m-30) cc_final: 0.8597 (m-30) REVERT: C 73 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7892 (p0) REVERT: C 256 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8348 (mp0) REVERT: C 265 LYS cc_start: 0.9354 (mttm) cc_final: 0.9030 (mtpt) REVERT: C 302 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7802 (mmtt) REVERT: C 306 TYR cc_start: 0.9045 (m-80) cc_final: 0.8688 (m-80) REVERT: C 334 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5567 (tpm170) REVERT: C 446 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.7668 (t-100) REVERT: C 554 MET cc_start: 0.8577 (tpp) cc_final: 0.8184 (tpp) REVERT: C 555 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 559 SER cc_start: 0.8880 (m) cc_final: 0.8672 (t) REVERT: C 567 ASN cc_start: 0.8526 (t0) cc_final: 0.8106 (t0) REVERT: C 578 MET cc_start: 0.7556 (mmp) cc_final: 0.7099 (mmm) REVERT: C 608 PHE cc_start: 0.4960 (OUTLIER) cc_final: 0.3616 (m-80) REVERT: C 713 MET cc_start: 0.8839 (tpp) cc_final: 0.8566 (tpt) REVERT: C 732 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8279 (tppt) REVERT: C 737 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: C 774 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8779 (mt-10) REVERT: C 792 ASP cc_start: 0.8828 (m-30) cc_final: 0.8601 (m-30) outliers start: 48 outliers final: 24 residues processed: 245 average time/residue: 0.4145 time to fit residues: 111.8422 Evaluate side-chains 246 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 446 TRP Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 732 LYS Chi-restraints excluded: chain C residue 737 GLU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.143264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095001 restraints weight = 12475.213| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.88 r_work: 0.2914 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.308 9766 Z= 0.445 Angle : 1.382 59.200 13312 Z= 0.857 Chirality : 0.061 1.006 1574 Planarity : 0.005 0.111 1604 Dihedral : 5.352 50.737 1640 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.31 % Allowed : 25.49 % Favored : 70.20 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.24), residues: 1114 helix: 1.93 (0.23), residues: 490 sheet: 1.34 (0.29), residues: 270 loop : -1.13 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 523 TYR 0.021 0.001 TYR A 568 PHE 0.011 0.001 PHE A 573 TRP 0.008 0.001 TRP A 106 HIS 0.002 0.001 HIS C 504 Details of bonding type rmsd covalent geometry : bond 0.00902 ( 9732) covalent geometry : angle 1.38066 (13236) SS BOND : bond 0.00124 ( 8) SS BOND : angle 0.62629 ( 16) hydrogen bonds : bond 0.03687 ( 488) hydrogen bonds : angle 3.79694 ( 1398) metal coordination : bond 0.00200 ( 6) link_BETA1-4 : bond 0.00488 ( 12) link_BETA1-4 : angle 1.74502 ( 36) link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 1.83431 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.10 seconds wall clock time: 57 minutes 33.48 seconds (3453.48 seconds total)