Starting phenix.real_space_refine on Tue May 13 00:48:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcx_37113/05_2025/8kcx_37113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcx_37113/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kcx_37113/05_2025/8kcx_37113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcx_37113/05_2025/8kcx_37113.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcx_37113/05_2025/8kcx_37113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcx_37113/05_2025/8kcx_37113.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.92, per 1000 atoms: 0.62 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.64 Time building geometry restraints manager: 3.08 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: 0.04 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 25.720 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP A 106 HIS 0.007 0.001 HIS A 504 PHE 0.012 0.001 PHE C 454 TYR 0.016 0.001 TYR C 724 ARG 0.002 0.000 ARG C 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 8) link_NAG-ASN : angle 3.40941 ( 24) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 1.45810 ( 36) hydrogen bonds : bond 0.26077 ( 488) hydrogen bonds : angle 8.60234 ( 1398) metal coordination : bond 0.09927 ( 6) SS BOND : bond 0.00163 ( 8) SS BOND : angle 0.78465 ( 16) covalent geometry : bond 0.00522 ( 9732) covalent geometry : angle 0.76920 (13236) *********************** 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 : 0.960 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: 0.9243 time to fit residues: 284.7108 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 : 0.922 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.145314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095394 restraints weight = 12403.386| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.82 r_work: 0.2927 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9766 Z= 0.158 Angle : 0.646 8.878 13312 Z= 0.312 Chirality : 0.045 0.265 1574 Planarity : 0.004 0.038 1604 Dihedral : 14.909 83.602 1644 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.80 % Allowed : 20.49 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.23), residues: 1114 helix: -0.65 (0.21), residues: 490 sheet: 1.26 (0.30), residues: 270 loop : -1.49 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 106 HIS 0.004 0.001 HIS A 504 PHE 0.011 0.001 PHE C 545 TYR 0.012 0.001 TYR C 188 ARG 0.005 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 8) link_NAG-ASN : angle 2.16890 ( 24) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 2.27846 ( 36) hydrogen bonds : bond 0.04820 ( 488) hydrogen bonds : angle 4.66286 ( 1398) metal coordination : bond 0.00628 ( 6) SS BOND : bond 0.00104 ( 8) SS BOND : angle 0.73539 ( 16) covalent geometry : bond 0.00346 ( 9732) covalent geometry : angle 0.62916 (13236) *********************** 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 291 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8388 (mp10) cc_final: 0.8154 (mm-40) REVERT: A 256 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8424 (mp0) REVERT: A 265 LYS cc_start: 0.9316 (mttm) cc_final: 0.9015 (mtpt) REVERT: A 334 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5924 (tpm170) REVERT: A 446 TRP cc_start: 0.8080 (OUTLIER) cc_final: 0.7574 (t-100) REVERT: A 554 MET cc_start: 0.8659 (tpp) cc_final: 0.8287 (tpp) REVERT: A 559 SER cc_start: 0.8953 (m) cc_final: 0.8632 (t) REVERT: A 713 MET cc_start: 0.8925 (tpp) cc_final: 0.8688 (tpt) REVERT: A 737 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 754 TRP cc_start: 0.9218 (m100) cc_final: 0.9012 (m100) REVERT: A 774 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 123 GLN cc_start: 0.8385 (mp10) cc_final: 0.8154 (mm-40) REVERT: C 256 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8411 (mp0) REVERT: C 265 LYS cc_start: 0.9319 (mttm) cc_final: 0.9022 (mtpt) REVERT: C 334 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5927 (tpm170) REVERT: C 446 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7572 (t-100) REVERT: C 554 MET cc_start: 0.8664 (tpp) cc_final: 0.8292 (tpp) REVERT: C 559 SER cc_start: 0.8950 (m) cc_final: 0.8630 (t) REVERT: C 713 MET cc_start: 0.8929 (tpp) cc_final: 0.8689 (tpt) REVERT: C 737 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: C 754 TRP cc_start: 0.9209 (m100) cc_final: 0.9002 (m100) REVERT: C 774 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8808 (mt-10) outliers start: 49 outliers final: 24 residues processed: 264 average time/residue: 0.8296 time to fit residues: 240.3206 Evaluate side-chains 260 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 220 ILE Chi-restraints excluded: chain A residue 307 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 581 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 732 LYS 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 104 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 307 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 581 ILE Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 732 LYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 C 121 ASN C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095165 restraints weight = 12582.706| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.23 r_work: 0.2891 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9766 Z= 0.207 Angle : 0.631 8.240 13312 Z= 0.305 Chirality : 0.046 0.289 1574 Planarity : 0.003 0.036 1604 Dihedral : 10.516 68.929 1640 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.78 % Allowed : 22.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1114 helix: 0.53 (0.22), residues: 490 sheet: 1.18 (0.29), residues: 270 loop : -1.39 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 106 HIS 0.004 0.001 HIS C 522 PHE 0.025 0.001 PHE A 312 TYR 0.014 0.001 TYR A 728 ARG 0.005 0.000 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 8) link_NAG-ASN : angle 2.18953 ( 24) link_BETA1-4 : bond 0.00533 ( 12) link_BETA1-4 : angle 2.09788 ( 36) hydrogen bonds : bond 0.04521 ( 488) hydrogen bonds : angle 4.29808 ( 1398) metal coordination : bond 0.00682 ( 6) SS BOND : bond 0.00142 ( 8) SS BOND : angle 0.68959 ( 16) covalent geometry : bond 0.00478 ( 9732) covalent geometry : angle 0.61573 (13236) *********************** 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 287 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8673 (mp10) cc_final: 0.8426 (mm-40) REVERT: A 256 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8425 (mp0) REVERT: A 265 LYS cc_start: 0.9371 (mttm) cc_final: 0.9008 (mtpt) REVERT: A 302 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.7972 (mmmt) REVERT: A 334 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5977 (tpm170) REVERT: A 446 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.7825 (t-100) REVERT: A 554 MET cc_start: 0.8711 (tpp) cc_final: 0.8287 (tpp) REVERT: A 559 SER cc_start: 0.8992 (m) cc_final: 0.8708 (t) REVERT: A 578 MET cc_start: 0.7625 (mmp) cc_final: 0.7169 (mmm) REVERT: A 713 MET cc_start: 0.8920 (tpp) cc_final: 0.8578 (tpt) REVERT: A 718 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 774 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8873 (mt-10) REVERT: C 123 GLN cc_start: 0.8665 (mp10) cc_final: 0.8420 (mm-40) REVERT: C 256 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8421 (mp0) REVERT: C 265 LYS cc_start: 0.9366 (mttm) cc_final: 0.9004 (mtpt) REVERT: C 302 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7969 (mmmt) REVERT: C 334 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.5980 (tpm170) REVERT: C 446 TRP cc_start: 0.8072 (OUTLIER) cc_final: 0.7827 (t-100) REVERT: C 554 MET cc_start: 0.8716 (tpp) cc_final: 0.8294 (tpp) REVERT: C 559 SER cc_start: 0.8990 (m) cc_final: 0.8705 (t) REVERT: C 578 MET cc_start: 0.7640 (mmp) cc_final: 0.7180 (mmm) REVERT: C 713 MET cc_start: 0.8923 (tpp) cc_final: 0.8578 (tpt) REVERT: C 718 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8070 (mp) REVERT: C 774 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8873 (mt-10) outliers start: 59 outliers final: 30 residues processed: 260 average time/residue: 0.8375 time to fit residues: 238.1925 Evaluate side-chains 250 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 453 VAL 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 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 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 220 ILE 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 453 VAL 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 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 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 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.141559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091903 restraints weight = 12384.529| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.86 r_work: 0.2871 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 9766 Z= 0.246 Angle : 0.630 9.109 13312 Z= 0.306 Chirality : 0.047 0.278 1574 Planarity : 0.003 0.034 1604 Dihedral : 8.052 59.050 1640 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 7.25 % Allowed : 21.76 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1114 helix: 0.89 (0.23), residues: 488 sheet: 1.12 (0.29), residues: 268 loop : -1.25 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 106 HIS 0.005 0.001 HIS A 522 PHE 0.015 0.001 PHE C 509 TYR 0.014 0.001 TYR C 188 ARG 0.003 0.000 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 1.94011 ( 24) link_BETA1-4 : bond 0.00511 ( 12) link_BETA1-4 : angle 2.40794 ( 36) hydrogen bonds : bond 0.04178 ( 488) hydrogen bonds : angle 4.18058 ( 1398) metal coordination : bond 0.00628 ( 6) SS BOND : bond 0.00182 ( 8) SS BOND : angle 0.74991 ( 16) covalent geometry : bond 0.00573 ( 9732) covalent geometry : angle 0.61321 (13236) *********************** 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 292 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 218 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8417 (mp0) REVERT: A 265 LYS cc_start: 0.9369 (mttm) cc_final: 0.9011 (mtpt) REVERT: A 302 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7968 (mmmt) REVERT: A 306 TYR cc_start: 0.9197 (m-80) cc_final: 0.8889 (m-80) REVERT: A 334 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5789 (tpm170) REVERT: A 446 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7894 (t-100) REVERT: A 554 MET cc_start: 0.8744 (tpp) cc_final: 0.8265 (tpp) REVERT: A 559 SER cc_start: 0.9002 (m) cc_final: 0.8708 (t) REVERT: A 567 ASN cc_start: 0.8750 (t0) cc_final: 0.8322 (t0) REVERT: A 608 PHE cc_start: 0.4921 (OUTLIER) cc_final: 0.3552 (m-80) REVERT: A 713 MET cc_start: 0.8870 (tpp) cc_final: 0.8544 (tpt) REVERT: A 718 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 737 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: A 774 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8866 (mt-10) REVERT: C 123 GLN cc_start: 0.8705 (mp10) cc_final: 0.8017 (mm-40) REVERT: C 256 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8416 (mp0) REVERT: C 265 LYS cc_start: 0.9365 (mttm) cc_final: 0.9010 (mtpt) REVERT: C 302 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7960 (mmmt) REVERT: C 306 TYR cc_start: 0.9200 (m-80) cc_final: 0.8891 (m-80) REVERT: C 334 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5791 (tpm170) REVERT: C 446 TRP cc_start: 0.8125 (OUTLIER) cc_final: 0.7896 (t-100) REVERT: C 554 MET cc_start: 0.8739 (tpp) cc_final: 0.8263 (tpp) REVERT: C 559 SER cc_start: 0.9006 (m) cc_final: 0.8712 (t) REVERT: C 567 ASN cc_start: 0.8751 (t0) cc_final: 0.8324 (t0) REVERT: C 608 PHE cc_start: 0.4922 (OUTLIER) cc_final: 0.3544 (m-80) REVERT: C 713 MET cc_start: 0.8872 (tpp) cc_final: 0.8543 (tpt) REVERT: C 718 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8110 (mp) REVERT: C 737 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: C 774 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8878 (mt-10) outliers start: 74 outliers final: 42 residues processed: 264 average time/residue: 0.7765 time to fit residues: 226.1721 Evaluate side-chains 258 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 VAL 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 453 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 467 GLN 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 557 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR 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 740 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 786 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 295 VAL 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 453 VAL Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 467 GLN 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 557 VAL Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR 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 740 LEU Chi-restraints excluded: chain C residue 758 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 84 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 475 ASN C 572 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093708 restraints weight = 12323.184| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.86 r_work: 0.2898 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9766 Z= 0.151 Angle : 0.590 8.992 13312 Z= 0.283 Chirality : 0.044 0.264 1574 Planarity : 0.003 0.036 1604 Dihedral : 7.346 52.246 1640 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.88 % Allowed : 24.41 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1114 helix: 1.15 (0.23), residues: 488 sheet: 1.20 (0.29), residues: 268 loop : -1.20 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 106 HIS 0.002 0.001 HIS C 522 PHE 0.008 0.001 PHE C 258 TYR 0.020 0.001 TYR A 568 ARG 0.005 0.000 ARG A 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 8) link_NAG-ASN : angle 1.83823 ( 24) link_BETA1-4 : bond 0.00503 ( 12) link_BETA1-4 : angle 2.27075 ( 36) hydrogen bonds : bond 0.03903 ( 488) hydrogen bonds : angle 4.05392 ( 1398) metal coordination : bond 0.00343 ( 6) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.71486 ( 16) covalent geometry : bond 0.00345 ( 9732) covalent geometry : angle 0.57371 (13236) *********************** 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 272 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8430 (mp0) REVERT: A 265 LYS cc_start: 0.9350 (mttm) cc_final: 0.9037 (mtpt) REVERT: A 302 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7932 (mmmt) REVERT: A 306 TYR cc_start: 0.9159 (m-80) cc_final: 0.8849 (m-80) REVERT: A 334 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5748 (tpm170) REVERT: A 446 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.7667 (t-100) REVERT: A 554 MET cc_start: 0.8696 (tpp) cc_final: 0.8225 (tpp) REVERT: A 559 SER cc_start: 0.8991 (m) cc_final: 0.8713 (t) REVERT: A 567 ASN cc_start: 0.8718 (t0) cc_final: 0.8448 (t160) REVERT: A 572 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: A 578 MET cc_start: 0.7515 (mmp) cc_final: 0.7141 (mmm) REVERT: A 608 PHE cc_start: 0.4900 (OUTLIER) cc_final: 0.3575 (m-80) REVERT: A 713 MET cc_start: 0.8922 (tpp) cc_final: 0.8592 (tpt) REVERT: A 774 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 123 GLN cc_start: 0.8628 (mp10) cc_final: 0.7969 (mm-40) REVERT: C 256 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8421 (mp0) REVERT: C 265 LYS cc_start: 0.9349 (mttm) cc_final: 0.9036 (mtpt) REVERT: C 302 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7921 (mmmt) REVERT: C 306 TYR cc_start: 0.9159 (m-80) cc_final: 0.8848 (m-80) REVERT: C 334 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5750 (tpm170) REVERT: C 446 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.7690 (t-100) REVERT: C 554 MET cc_start: 0.8680 (tpp) cc_final: 0.8211 (tpp) REVERT: C 559 SER cc_start: 0.8995 (m) cc_final: 0.8715 (t) REVERT: C 567 ASN cc_start: 0.8724 (t0) cc_final: 0.8459 (t160) REVERT: C 572 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8591 (mp10) REVERT: C 578 MET cc_start: 0.7526 (mmp) cc_final: 0.7154 (mmm) REVERT: C 608 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3566 (m-80) REVERT: C 713 MET cc_start: 0.8930 (tpp) cc_final: 0.8591 (tpt) REVERT: C 774 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8821 (mt-10) REVERT: C 792 ASP cc_start: 0.8982 (m-30) cc_final: 0.8421 (m-30) outliers start: 60 outliers final: 36 residues processed: 246 average time/residue: 0.7603 time to fit residues: 206.5992 Evaluate side-chains 252 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 462 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU 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 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 462 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL 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 716 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 786 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 C 467 GLN C 475 ASN C 572 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094831 restraints weight = 12363.754| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.25 r_work: 0.2894 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9766 Z= 0.151 Angle : 0.574 9.054 13312 Z= 0.275 Chirality : 0.044 0.262 1574 Planarity : 0.003 0.036 1604 Dihedral : 6.588 50.423 1640 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 6.57 % Allowed : 23.92 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1114 helix: 1.37 (0.23), residues: 488 sheet: 1.23 (0.29), residues: 270 loop : -1.14 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.003 0.001 HIS A 504 PHE 0.014 0.001 PHE A 509 TYR 0.013 0.001 TYR A 188 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 8) link_NAG-ASN : angle 1.75127 ( 24) link_BETA1-4 : bond 0.00494 ( 12) link_BETA1-4 : angle 2.15137 ( 36) hydrogen bonds : bond 0.03756 ( 488) hydrogen bonds : angle 3.96577 ( 1398) metal coordination : bond 0.00357 ( 6) SS BOND : bond 0.00142 ( 8) SS BOND : angle 0.71080 ( 16) covalent geometry : bond 0.00347 ( 9732) covalent geometry : angle 0.55960 (13236) *********************** 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 283 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 1.027 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: 0.9047 (mt-10) cc_final: 0.8439 (mp0) REVERT: A 265 LYS cc_start: 0.9363 (mttm) cc_final: 0.9053 (mtpt) REVERT: A 302 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7916 (mmmt) REVERT: A 306 TYR cc_start: 0.9104 (m-80) cc_final: 0.8797 (m-80) REVERT: A 334 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5645 (tpm170) REVERT: A 542 PHE cc_start: 0.7979 (m-10) cc_final: 0.7613 (m-10) REVERT: A 554 MET cc_start: 0.8699 (tpp) cc_final: 0.8236 (tpp) REVERT: A 559 SER cc_start: 0.8991 (m) cc_final: 0.8725 (t) REVERT: A 572 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8421 (mp10) REVERT: A 578 MET cc_start: 0.7526 (mmp) cc_final: 0.7113 (mmm) REVERT: A 608 PHE cc_start: 0.4904 (OUTLIER) cc_final: 0.3550 (m-80) REVERT: A 643 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7026 (mm) REVERT: A 713 MET cc_start: 0.8925 (tpp) cc_final: 0.8606 (tpt) REVERT: A 732 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7927 (mppt) REVERT: A 737 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 774 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8830 (mt-10) REVERT: C 123 GLN cc_start: 0.8672 (mp10) cc_final: 0.8030 (mm-40) REVERT: C 256 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8433 (mp0) REVERT: C 265 LYS cc_start: 0.9363 (mttm) cc_final: 0.9009 (mtpt) REVERT: C 302 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7911 (mmmt) REVERT: C 306 TYR cc_start: 0.9102 (m-80) cc_final: 0.8793 (m-80) REVERT: C 334 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5643 (tpm170) REVERT: C 542 PHE cc_start: 0.7963 (m-10) cc_final: 0.7596 (m-10) REVERT: C 554 MET cc_start: 0.8692 (tpp) cc_final: 0.8236 (tpp) REVERT: C 559 SER cc_start: 0.8998 (m) cc_final: 0.8732 (t) REVERT: C 572 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: C 578 MET cc_start: 0.7537 (mmp) cc_final: 0.7126 (mmm) REVERT: C 608 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.3545 (m-80) REVERT: C 643 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7030 (mm) REVERT: C 713 MET cc_start: 0.8932 (tpp) cc_final: 0.8606 (tpt) REVERT: C 732 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7936 (mppt) REVERT: C 737 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: C 774 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8841 (mt-10) REVERT: C 783 ILE cc_start: 0.8991 (pp) cc_final: 0.8788 (pp) outliers start: 67 outliers final: 34 residues processed: 260 average time/residue: 0.7959 time to fit residues: 229.0476 Evaluate side-chains 256 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 467 GLN Chi-restraints excluded: chain A residue 498 ILE 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 581 ILE Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ASN 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 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 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 467 GLN Chi-restraints excluded: chain C residue 498 ILE 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 581 ILE Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 720 ASN 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 786 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.0370 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 567 ASN A 572 GLN C 467 GLN C 475 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN C 572 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094528 restraints weight = 12347.718| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.87 r_work: 0.2909 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3052 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= 0.137 Angle : 0.573 9.260 13312 Z= 0.276 Chirality : 0.043 0.258 1574 Planarity : 0.003 0.034 1604 Dihedral : 6.084 50.517 1640 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 6.27 % Allowed : 24.02 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1114 helix: 1.53 (0.23), residues: 490 sheet: 1.28 (0.29), residues: 270 loop : -1.09 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.005 0.001 HIS C 504 PHE 0.013 0.001 PHE A 509 TYR 0.023 0.001 TYR C 568 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 1.73411 ( 24) link_BETA1-4 : bond 0.00480 ( 12) link_BETA1-4 : angle 2.01720 ( 36) hydrogen bonds : bond 0.03649 ( 488) hydrogen bonds : angle 3.89646 ( 1398) metal coordination : bond 0.00293 ( 6) SS BOND : bond 0.00133 ( 8) SS BOND : angle 0.69788 ( 16) covalent geometry : bond 0.00311 ( 9732) covalent geometry : angle 0.55940 (13236) *********************** 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 277 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 1.065 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: 0.9039 (mt-10) cc_final: 0.8435 (mp0) REVERT: A 265 LYS cc_start: 0.9351 (mttm) cc_final: 0.9041 (mtpt) REVERT: A 302 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7886 (mmmt) REVERT: A 306 TYR cc_start: 0.9071 (m-80) cc_final: 0.8738 (m-80) REVERT: A 334 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5638 (tpm170) REVERT: A 446 TRP cc_start: 0.8102 (t60) cc_final: 0.7834 (t-100) REVERT: A 542 PHE cc_start: 0.8002 (m-10) cc_final: 0.7662 (m-10) REVERT: A 554 MET cc_start: 0.8693 (tpp) cc_final: 0.8234 (tpp) REVERT: A 559 SER cc_start: 0.8947 (m) cc_final: 0.8688 (t) REVERT: A 578 MET cc_start: 0.7564 (mmp) cc_final: 0.7197 (mmm) REVERT: A 608 PHE cc_start: 0.4931 (OUTLIER) cc_final: 0.3635 (m-80) REVERT: A 713 MET cc_start: 0.8924 (tpp) cc_final: 0.8632 (tpt) REVERT: A 732 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7986 (mppt) REVERT: A 737 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: A 774 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8810 (mt-10) REVERT: C 123 GLN cc_start: 0.8638 (mp10) cc_final: 0.8009 (mm-40) REVERT: C 256 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8430 (mp0) REVERT: C 265 LYS cc_start: 0.9351 (mttm) cc_final: 0.9043 (mtpt) REVERT: C 302 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7871 (mmmt) REVERT: C 306 TYR cc_start: 0.9071 (m-80) cc_final: 0.8740 (m-80) REVERT: C 334 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5634 (tpm170) REVERT: C 446 TRP cc_start: 0.8043 (t60) cc_final: 0.7753 (t-100) REVERT: C 542 PHE cc_start: 0.7991 (m-10) cc_final: 0.7648 (m-10) REVERT: C 554 MET cc_start: 0.8684 (tpp) cc_final: 0.8230 (tpp) REVERT: C 559 SER cc_start: 0.8945 (m) cc_final: 0.8683 (t) REVERT: C 578 MET cc_start: 0.7557 (mmp) cc_final: 0.7192 (mmm) REVERT: C 608 PHE cc_start: 0.4929 (OUTLIER) cc_final: 0.3626 (m-80) REVERT: C 713 MET cc_start: 0.8927 (tpp) cc_final: 0.8630 (tpt) REVERT: C 732 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7991 (mppt) REVERT: C 737 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: C 774 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8819 (mt-10) REVERT: C 783 ILE cc_start: 0.8936 (pp) cc_final: 0.8667 (pp) outliers start: 64 outliers final: 37 residues processed: 253 average time/residue: 0.7812 time to fit residues: 218.0433 Evaluate side-chains 249 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 VAL Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 466 TYR Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 581 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 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 786 ASP Chi-restraints excluded: chain A residue 793 ILE 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 295 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 466 TYR Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 581 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 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 786 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 475 ASN A 567 ASN A 764 ASN C 467 GLN C 567 ASN C 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094501 restraints weight = 12439.994| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.78 r_work: 0.2914 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9766 Z= 0.159 Angle : 0.594 9.553 13312 Z= 0.285 Chirality : 0.044 0.256 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.680 50.414 1640 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 5.69 % Allowed : 24.80 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1114 helix: 1.65 (0.23), residues: 490 sheet: 1.30 (0.29), residues: 270 loop : -1.04 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS A 504 PHE 0.013 0.001 PHE C 509 TYR 0.021 0.001 TYR A 568 ARG 0.005 0.000 ARG A 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 8) link_NAG-ASN : angle 1.71839 ( 24) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 1.85396 ( 36) hydrogen bonds : bond 0.03640 ( 488) hydrogen bonds : angle 3.86139 ( 1398) metal coordination : bond 0.00377 ( 6) SS BOND : bond 0.00142 ( 8) SS BOND : angle 0.70357 ( 16) covalent geometry : bond 0.00371 ( 9732) covalent geometry : angle 0.58305 (13236) *********************** 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 270 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.945 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: 0.9031 (mt-10) cc_final: 0.8428 (mp0) REVERT: A 265 LYS cc_start: 0.9347 (mttm) cc_final: 0.9023 (mtpt) REVERT: A 302 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7860 (mmmt) REVERT: A 306 TYR cc_start: 0.9065 (m-80) cc_final: 0.8714 (m-80) REVERT: A 334 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5674 (tpm170) REVERT: A 446 TRP cc_start: 0.8116 (t60) cc_final: 0.7827 (t-100) REVERT: A 542 PHE cc_start: 0.8004 (m-10) cc_final: 0.7681 (m-10) REVERT: A 554 MET cc_start: 0.8700 (tpp) cc_final: 0.8247 (tpp) REVERT: A 559 SER cc_start: 0.8928 (m) cc_final: 0.8688 (t) REVERT: A 578 MET cc_start: 0.7543 (mmp) cc_final: 0.7169 (mmm) REVERT: A 608 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.3515 (m-80) REVERT: A 713 MET cc_start: 0.8905 (tpp) cc_final: 0.8629 (tpt) REVERT: A 732 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7978 (mppt) REVERT: A 737 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 774 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8810 (mt-10) REVERT: C 123 GLN cc_start: 0.8641 (mp10) cc_final: 0.8017 (mm-40) REVERT: C 256 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8412 (mp0) REVERT: C 265 LYS cc_start: 0.9349 (mttm) cc_final: 0.9028 (mtpt) REVERT: C 302 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7840 (mmmt) REVERT: C 306 TYR cc_start: 0.9065 (m-80) cc_final: 0.8713 (m-80) REVERT: C 334 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5670 (tpm170) REVERT: C 446 TRP cc_start: 0.8123 (t60) cc_final: 0.7852 (t-100) REVERT: C 542 PHE cc_start: 0.7993 (m-10) cc_final: 0.7669 (m-10) REVERT: C 554 MET cc_start: 0.8697 (tpp) cc_final: 0.8247 (tpp) REVERT: C 559 SER cc_start: 0.8925 (m) cc_final: 0.8682 (t) REVERT: C 578 MET cc_start: 0.7557 (mmp) cc_final: 0.7181 (mmm) REVERT: C 608 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.3517 (m-80) REVERT: C 713 MET cc_start: 0.8907 (tpp) cc_final: 0.8627 (tpt) REVERT: C 732 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7980 (mppt) REVERT: C 737 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: C 774 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8826 (mt-10) REVERT: C 783 ILE cc_start: 0.8942 (pp) cc_final: 0.8705 (pp) outliers start: 58 outliers final: 34 residues processed: 248 average time/residue: 0.7493 time to fit residues: 205.5669 Evaluate side-chains 262 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 310 SER Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 498 ILE 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 557 VAL Chi-restraints excluded: chain A residue 581 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 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 310 SER Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 498 ILE 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 557 VAL Chi-restraints excluded: chain C residue 581 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 12 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 475 ASN C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095880 restraints weight = 12264.377| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.84 r_work: 0.2933 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9766 Z= 0.119 Angle : 0.578 9.678 13312 Z= 0.277 Chirality : 0.043 0.247 1574 Planarity : 0.003 0.033 1604 Dihedral : 5.376 50.635 1640 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.41 % Allowed : 26.18 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1114 helix: 1.85 (0.23), residues: 490 sheet: 1.37 (0.29), residues: 270 loop : -1.01 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.004 0.001 HIS A 504 PHE 0.006 0.001 PHE C 258 TYR 0.020 0.001 TYR C 568 ARG 0.004 0.000 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 8) link_NAG-ASN : angle 1.76362 ( 24) link_BETA1-4 : bond 0.00486 ( 12) link_BETA1-4 : angle 1.75531 ( 36) hydrogen bonds : bond 0.03461 ( 488) hydrogen bonds : angle 3.75920 ( 1398) metal coordination : bond 0.00238 ( 6) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.71138 ( 16) covalent geometry : bond 0.00272 ( 9732) covalent geometry : angle 0.56697 (13236) *********************** 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 273 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.974 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: 0.9035 (mt-10) cc_final: 0.8414 (mp0) REVERT: A 265 LYS cc_start: 0.9339 (mttm) cc_final: 0.9015 (mtpt) REVERT: A 302 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7826 (mmmt) REVERT: A 306 TYR cc_start: 0.8987 (m-80) cc_final: 0.8609 (m-80) REVERT: A 334 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5573 (tpm170) REVERT: A 446 TRP cc_start: 0.8043 (t60) cc_final: 0.7798 (t-100) REVERT: A 542 PHE cc_start: 0.8024 (m-10) cc_final: 0.7695 (m-10) REVERT: A 554 MET cc_start: 0.8699 (tpp) cc_final: 0.8213 (tpp) REVERT: A 559 SER cc_start: 0.8939 (m) cc_final: 0.8731 (t) REVERT: A 578 MET cc_start: 0.7501 (mmp) cc_final: 0.7034 (mmm) REVERT: A 608 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.3564 (m-80) REVERT: A 713 MET cc_start: 0.8894 (tpp) cc_final: 0.8615 (tpt) REVERT: A 732 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8012 (mppt) REVERT: A 737 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 774 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8772 (mt-10) REVERT: A 792 ASP cc_start: 0.8844 (m-30) cc_final: 0.8576 (m-30) REVERT: C 123 GLN cc_start: 0.8603 (mp10) cc_final: 0.7986 (mm-40) REVERT: C 256 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8405 (mp0) REVERT: C 265 LYS cc_start: 0.9342 (mttm) cc_final: 0.9019 (mtpt) REVERT: C 302 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7820 (mmmt) REVERT: C 306 TYR cc_start: 0.9035 (m-80) cc_final: 0.8675 (m-80) REVERT: C 334 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5568 (tpm170) REVERT: C 446 TRP cc_start: 0.8074 (t60) cc_final: 0.7814 (t-100) REVERT: C 542 PHE cc_start: 0.8015 (m-10) cc_final: 0.7685 (m-10) REVERT: C 554 MET cc_start: 0.8688 (tpp) cc_final: 0.8206 (tpp) REVERT: C 559 SER cc_start: 0.8937 (m) cc_final: 0.8723 (t) REVERT: C 578 MET cc_start: 0.7470 (mmp) cc_final: 0.6989 (mmm) REVERT: C 608 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.3560 (m-80) REVERT: C 713 MET cc_start: 0.8898 (tpp) cc_final: 0.8615 (tpt) REVERT: C 732 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8018 (mppt) REVERT: C 737 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: C 774 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8779 (mt-10) REVERT: C 783 ILE cc_start: 0.8893 (pp) cc_final: 0.8595 (pp) outliers start: 45 outliers final: 27 residues processed: 256 average time/residue: 0.8345 time to fit residues: 234.4456 Evaluate side-chains 252 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 498 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL 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 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 498 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL 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 72 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.0050 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 A 475 ASN C 178 HIS C 467 GLN C 475 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095360 restraints weight = 12547.820| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.88 r_work: 0.2925 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9766 Z= 0.119 Angle : 0.592 9.770 13312 Z= 0.287 Chirality : 0.043 0.247 1574 Planarity : 0.003 0.033 1604 Dihedral : 5.240 50.607 1640 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.63 % Allowed : 27.25 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1114 helix: 1.92 (0.23), residues: 490 sheet: 1.42 (0.29), residues: 270 loop : -0.99 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 106 HIS 0.005 0.001 HIS C 504 PHE 0.021 0.001 PHE C 509 TYR 0.021 0.001 TYR C 568 ARG 0.005 0.000 ARG A 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 8) link_NAG-ASN : angle 1.76213 ( 24) link_BETA1-4 : bond 0.00466 ( 12) link_BETA1-4 : angle 1.70836 ( 36) hydrogen bonds : bond 0.03415 ( 488) hydrogen bonds : angle 3.72532 ( 1398) metal coordination : bond 0.00168 ( 6) SS BOND : bond 0.00113 ( 8) SS BOND : angle 0.68075 ( 16) covalent geometry : bond 0.00271 ( 9732) covalent geometry : angle 0.58170 (13236) ********************** 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 243 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.001 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: 0.9026 (mt-10) cc_final: 0.8379 (mp0) REVERT: A 265 LYS cc_start: 0.9361 (mttm) cc_final: 0.9038 (mtpt) REVERT: A 306 TYR cc_start: 0.8932 (m-80) cc_final: 0.8641 (m-80) REVERT: A 334 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5593 (tpm170) REVERT: A 446 TRP cc_start: 0.8038 (t60) cc_final: 0.7744 (t-100) REVERT: A 554 MET cc_start: 0.8675 (tpp) cc_final: 0.8200 (tpp) REVERT: A 567 ASN cc_start: 0.8502 (t0) cc_final: 0.8015 (t0) REVERT: A 578 MET cc_start: 0.7543 (mmp) cc_final: 0.7063 (mmm) REVERT: A 608 PHE cc_start: 0.5236 (OUTLIER) cc_final: 0.3849 (m-80) REVERT: A 713 MET cc_start: 0.8889 (tpp) cc_final: 0.8617 (tpt) REVERT: A 732 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8022 (mppt) REVERT: A 737 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 763 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8506 (mm-40) REVERT: A 774 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8760 (mt-10) REVERT: A 792 ASP cc_start: 0.8838 (m-30) cc_final: 0.8559 (m-30) REVERT: C 123 GLN cc_start: 0.8589 (mp10) cc_final: 0.7959 (mm-40) REVERT: C 256 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8362 (mp0) REVERT: C 265 LYS cc_start: 0.9362 (mttm) cc_final: 0.9037 (mtpt) REVERT: C 306 TYR cc_start: 0.8933 (m-80) cc_final: 0.8636 (m-80) REVERT: C 334 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.5591 (tpm170) REVERT: C 446 TRP cc_start: 0.8041 (t60) cc_final: 0.7741 (t-100) REVERT: C 554 MET cc_start: 0.8676 (tpp) cc_final: 0.8203 (tpp) REVERT: C 559 SER cc_start: 0.8916 (m) cc_final: 0.8715 (t) REVERT: C 567 ASN cc_start: 0.8483 (t0) cc_final: 0.8022 (t0) REVERT: C 578 MET cc_start: 0.7548 (mmp) cc_final: 0.7040 (mmm) REVERT: C 608 PHE cc_start: 0.5237 (OUTLIER) cc_final: 0.3852 (m-80) REVERT: C 713 MET cc_start: 0.8889 (tpp) cc_final: 0.8614 (tpt) REVERT: C 732 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8023 (mppt) REVERT: C 737 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 774 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8759 (mt-10) REVERT: C 783 ILE cc_start: 0.8877 (pp) cc_final: 0.8587 (pp) outliers start: 37 outliers final: 23 residues processed: 234 average time/residue: 0.8428 time to fit residues: 215.8490 Evaluate side-chains 243 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 ARG Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 557 VAL 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 737 GLU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE 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 334 ARG Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 557 VAL 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 737 GLU 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 7 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 475 ASN C 467 GLN C 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093205 restraints weight = 12462.450| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.85 r_work: 0.2891 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9766 Z= 0.186 Angle : 0.613 9.565 13312 Z= 0.300 Chirality : 0.045 0.263 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.186 50.123 1640 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.71 % Allowed : 26.67 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1114 helix: 1.91 (0.23), residues: 490 sheet: 1.35 (0.29), residues: 270 loop : -0.96 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 106 HIS 0.004 0.001 HIS A 504 PHE 0.006 0.001 PHE A 717 TYR 0.022 0.001 TYR C 568 ARG 0.005 0.000 ARG C 523 Details of bonding type rmsd link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 1.77010 ( 24) link_BETA1-4 : bond 0.00433 ( 12) link_BETA1-4 : angle 1.62525 ( 36) hydrogen bonds : bond 0.03681 ( 488) hydrogen bonds : angle 3.83374 ( 1398) metal coordination : bond 0.00426 ( 6) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.66958 ( 16) covalent geometry : bond 0.00435 ( 9732) covalent geometry : angle 0.60380 (13236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6353.82 seconds wall clock time: 110 minutes 29.75 seconds (6629.75 seconds total)