Starting phenix.real_space_refine on Fri Mar 14 03:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcx_37113/03_2025/8kcx_37113.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcx_37113/03_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_37113/03_2025/8kcx_37113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcx_37113/03_2025/8kcx_37113.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcx_37113/03_2025/8kcx_37113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcx_37113/03_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-5624/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: 6.11, per 1000 atoms: 0.64 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: 2.61 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: 0.99 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: 2.84 Time building geometry restraints manager: 3.04 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 0.570 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: 0.070 Set scattering table: 0.110 Process input model: 26.710 Find NCS groups from input model: 0.400 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- 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 : 0.005 0.058 9732 Z= 0.334 Angle : 0.769 10.121 13236 Z= 0.434 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 *********************** 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 : 1.011 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: 0.9003 time to fit residues: 277.3330 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 : 0.998 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9990 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: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.144833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.095279 restraints weight = 12382.813| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.81 r_work: 0.2920 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9732 Z= 0.254 Angle : 0.643 9.197 13236 Z= 0.315 Chirality : 0.046 0.270 1574 Planarity : 0.004 0.037 1604 Dihedral : 14.537 82.555 1644 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.20 % Allowed : 20.10 % 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: -0.77 (0.23), residues: 1114 helix: -0.67 (0.21), residues: 490 sheet: 1.20 (0.30), residues: 270 loop : -1.48 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 106 HIS 0.005 0.001 HIS C 504 PHE 0.012 0.001 PHE A 608 TYR 0.013 0.001 TYR A 724 ARG 0.005 0.001 ARG A 518 *********************** 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 293 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8424 (mp10) cc_final: 0.8193 (mm-40) REVERT: A 256 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8434 (mp0) REVERT: A 265 LYS cc_start: 0.9325 (mttm) cc_final: 0.9020 (mtpt) REVERT: A 334 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.5809 (tpm170) REVERT: A 446 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.7584 (t-100) REVERT: A 554 MET cc_start: 0.8684 (tpp) cc_final: 0.8313 (tpp) REVERT: A 559 SER cc_start: 0.8956 (m) cc_final: 0.8633 (t) REVERT: A 713 MET cc_start: 0.8927 (tpp) cc_final: 0.8575 (tpt) REVERT: A 737 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: A 774 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8820 (mt-10) REVERT: C 123 GLN cc_start: 0.8416 (mp10) cc_final: 0.8186 (mm-40) REVERT: C 256 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8416 (mp0) REVERT: C 265 LYS cc_start: 0.9327 (mttm) cc_final: 0.9025 (mtpt) REVERT: C 334 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5810 (tpm170) REVERT: C 446 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7583 (t-100) REVERT: C 554 MET cc_start: 0.8687 (tpp) cc_final: 0.8318 (tpp) REVERT: C 559 SER cc_start: 0.8957 (m) cc_final: 0.8634 (t) REVERT: C 713 MET cc_start: 0.8932 (tpp) cc_final: 0.8573 (tpt) REVERT: C 737 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: C 774 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8829 (mt-10) outliers start: 53 outliers final: 26 residues processed: 266 average time/residue: 0.8728 time to fit residues: 253.8957 Evaluate side-chains 250 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 718 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 718 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: 0.0980 chunk 99 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN C 121 ASN C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.094509 restraints weight = 12539.991| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.86 r_work: 0.2912 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9732 Z= 0.218 Angle : 0.580 8.283 13236 Z= 0.281 Chirality : 0.045 0.276 1574 Planarity : 0.003 0.034 1604 Dihedral : 10.424 68.176 1640 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.59 % Allowed : 22.06 % Favored : 72.35 % 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: 0.13 (0.23), residues: 1114 helix: 0.50 (0.22), residues: 490 sheet: 1.25 (0.30), residues: 270 loop : -1.36 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 106 HIS 0.003 0.001 HIS C 504 PHE 0.024 0.001 PHE A 312 TYR 0.015 0.001 TYR C 568 ARG 0.004 0.000 ARG C 518 *********************** 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 273 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8593 (mp10) cc_final: 0.8344 (mm-40) REVERT: A 256 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8433 (mp0) REVERT: A 265 LYS cc_start: 0.9350 (mttm) cc_final: 0.9044 (mtpt) REVERT: A 302 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7962 (mmmt) REVERT: A 446 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7810 (t-100) REVERT: A 554 MET cc_start: 0.8659 (tpp) cc_final: 0.8226 (tpp) REVERT: A 559 SER cc_start: 0.8969 (m) cc_final: 0.8701 (t) REVERT: A 579 TYR cc_start: 0.6996 (m-10) cc_final: 0.6785 (m-10) REVERT: A 713 MET cc_start: 0.8912 (tpp) cc_final: 0.8606 (tpt) REVERT: A 754 TRP cc_start: 0.9101 (m100) cc_final: 0.8866 (m100) REVERT: A 774 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8825 (mt-10) REVERT: C 123 GLN cc_start: 0.8585 (mp10) cc_final: 0.8339 (mm-40) REVERT: C 256 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8418 (mp0) REVERT: C 265 LYS cc_start: 0.9351 (mttm) cc_final: 0.9046 (mtpt) REVERT: C 302 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7952 (mmmt) REVERT: C 446 TRP cc_start: 0.8064 (OUTLIER) cc_final: 0.7810 (t-100) REVERT: C 554 MET cc_start: 0.8650 (tpp) cc_final: 0.8221 (tpp) REVERT: C 559 SER cc_start: 0.8967 (m) cc_final: 0.8699 (t) REVERT: C 579 TYR cc_start: 0.6999 (m-10) cc_final: 0.6785 (m-10) REVERT: C 713 MET cc_start: 0.8920 (tpp) cc_final: 0.8610 (tpt) REVERT: C 754 TRP cc_start: 0.9095 (m100) cc_final: 0.8863 (m100) REVERT: C 774 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8826 (mt-10) outliers start: 57 outliers final: 36 residues processed: 244 average time/residue: 1.0052 time to fit residues: 269.7086 Evaluate side-chains 254 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 446 TRP Chi-restraints excluded: chain A residue 453 VAL 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 581 ILE Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 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 446 TRP Chi-restraints excluded: chain C residue 453 VAL 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 581 ILE Chi-restraints excluded: chain C residue 716 ILE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 725 LEU Chi-restraints excluded: chain C residue 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: 0.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 467 GLN A 572 GLN C 467 GLN C 572 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093426 restraints weight = 12351.298| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.82 r_work: 0.2901 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9732 Z= 0.302 Angle : 0.583 8.986 13236 Z= 0.284 Chirality : 0.046 0.277 1574 Planarity : 0.003 0.036 1604 Dihedral : 8.598 57.973 1640 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.37 % Allowed : 22.45 % Favored : 71.18 % 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: 0.46 (0.24), residues: 1114 helix: 0.91 (0.23), residues: 490 sheet: 1.24 (0.30), residues: 270 loop : -1.28 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 106 HIS 0.003 0.001 HIS C 522 PHE 0.012 0.001 PHE A 509 TYR 0.016 0.001 TYR C 568 ARG 0.003 0.000 ARG C 518 *********************** 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 287 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8636 (mp10) cc_final: 0.7922 (mm-40) REVERT: A 256 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8399 (mp0) REVERT: A 265 LYS cc_start: 0.9348 (mttm) cc_final: 0.8987 (mtpt) REVERT: A 302 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7924 (mmmt) REVERT: A 306 TYR cc_start: 0.9189 (m-80) cc_final: 0.8927 (m-80) REVERT: A 334 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5624 (tpm170) REVERT: A 446 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7870 (t-100) REVERT: A 554 MET cc_start: 0.8668 (tpp) cc_final: 0.8204 (tpp) REVERT: A 559 SER cc_start: 0.8976 (m) cc_final: 0.8700 (t) REVERT: A 572 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: A 578 MET cc_start: 0.7596 (mmp) cc_final: 0.7229 (mmm) REVERT: A 608 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3520 (m-80) REVERT: A 713 MET cc_start: 0.8898 (tpp) cc_final: 0.8599 (tpt) REVERT: A 718 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (mp) REVERT: A 754 TRP cc_start: 0.9128 (m100) cc_final: 0.8913 (m100) REVERT: A 774 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8819 (mt-10) REVERT: A 783 ILE cc_start: 0.8972 (pp) cc_final: 0.8746 (pp) REVERT: C 123 GLN cc_start: 0.8625 (mp10) cc_final: 0.7917 (mm-40) REVERT: C 256 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8398 (mp0) REVERT: C 265 LYS cc_start: 0.9340 (mttm) cc_final: 0.8979 (mtpt) REVERT: C 302 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7919 (mmmt) REVERT: C 306 TYR cc_start: 0.9188 (m-80) cc_final: 0.8928 (m-80) REVERT: C 334 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5624 (tpm170) REVERT: C 446 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7873 (t-100) REVERT: C 554 MET cc_start: 0.8660 (tpp) cc_final: 0.8201 (tpp) REVERT: C 559 SER cc_start: 0.8977 (m) cc_final: 0.8703 (t) REVERT: C 572 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: C 578 MET cc_start: 0.7607 (mmp) cc_final: 0.7238 (mmm) REVERT: C 608 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.3515 (m-80) REVERT: C 713 MET cc_start: 0.8901 (tpp) cc_final: 0.8596 (tpt) REVERT: C 718 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7994 (mp) REVERT: C 754 TRP cc_start: 0.9118 (m100) cc_final: 0.8909 (m100) REVERT: C 774 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8829 (mt-10) outliers start: 65 outliers final: 34 residues processed: 260 average time/residue: 0.8142 time to fit residues: 233.1326 Evaluate side-chains 272 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 498 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 572 GLN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 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 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 498 ILE Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 GLN Chi-restraints excluded: chain C residue 608 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093814 restraints weight = 12315.551| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.86 r_work: 0.2901 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9732 Z= 0.247 Angle : 0.570 9.040 13236 Z= 0.278 Chirality : 0.045 0.268 1574 Planarity : 0.003 0.036 1604 Dihedral : 7.730 59.207 1640 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 6.67 % Allowed : 24.12 % Favored : 69.22 % 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: 0.65 (0.24), residues: 1114 helix: 1.10 (0.23), residues: 502 sheet: 1.24 (0.29), residues: 270 loop : -1.22 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 106 HIS 0.003 0.001 HIS C 504 PHE 0.018 0.001 PHE C 312 TYR 0.013 0.001 TYR C 188 ARG 0.004 0.000 ARG A 523 *********************** 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 296 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8642 (mp10) cc_final: 0.7956 (mm-40) REVERT: A 207 GLU cc_start: 0.8988 (tt0) cc_final: 0.8769 (tt0) REVERT: A 256 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8414 (mp0) REVERT: A 265 LYS cc_start: 0.9352 (mttm) cc_final: 0.8998 (mtpt) REVERT: A 302 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7943 (mmmt) REVERT: A 306 TYR cc_start: 0.9157 (m-80) cc_final: 0.8862 (m-80) REVERT: A 334 ARG cc_start: 0.6129 (OUTLIER) cc_final: 0.5582 (tpm170) REVERT: A 446 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7617 (t-100) REVERT: A 542 PHE cc_start: 0.8034 (m-10) cc_final: 0.7692 (m-10) REVERT: A 554 MET cc_start: 0.8680 (tpp) cc_final: 0.8203 (tpp) REVERT: A 559 SER cc_start: 0.8977 (m) cc_final: 0.8718 (t) REVERT: A 578 MET cc_start: 0.7539 (mmp) cc_final: 0.7134 (mmm) REVERT: A 608 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.3545 (m-80) REVERT: A 713 MET cc_start: 0.8925 (tpp) cc_final: 0.8614 (tpt) REVERT: A 718 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 737 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: A 754 TRP cc_start: 0.9181 (m100) cc_final: 0.8970 (m100) REVERT: A 774 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8836 (mt-10) REVERT: A 783 ILE cc_start: 0.8952 (pp) cc_final: 0.8652 (pp) REVERT: C 123 GLN cc_start: 0.8634 (mp10) cc_final: 0.7955 (mm-40) REVERT: C 207 GLU cc_start: 0.8971 (tt0) cc_final: 0.8753 (tt0) REVERT: C 256 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8414 (mp0) REVERT: C 265 LYS cc_start: 0.9348 (mttm) cc_final: 0.9040 (mtpt) REVERT: C 302 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7942 (mmmt) REVERT: C 306 TYR cc_start: 0.9157 (m-80) cc_final: 0.8862 (m-80) REVERT: C 334 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5584 (tpm170) REVERT: C 446 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.7618 (t-100) REVERT: C 542 PHE cc_start: 0.8028 (m-10) cc_final: 0.7684 (m-10) REVERT: C 554 MET cc_start: 0.8663 (tpp) cc_final: 0.8192 (tpp) REVERT: C 559 SER cc_start: 0.8982 (m) cc_final: 0.8725 (t) REVERT: C 578 MET cc_start: 0.7562 (mmp) cc_final: 0.7154 (mmm) REVERT: C 608 PHE cc_start: 0.4910 (OUTLIER) cc_final: 0.3542 (m-80) REVERT: C 713 MET cc_start: 0.8929 (tpp) cc_final: 0.8616 (tpt) REVERT: C 718 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 737 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: C 754 TRP cc_start: 0.9180 (m100) cc_final: 0.8973 (m100) REVERT: C 774 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8841 (mt-10) REVERT: C 783 ILE cc_start: 0.8905 (pp) cc_final: 0.8670 (pp) outliers start: 68 outliers final: 38 residues processed: 272 average time/residue: 1.2539 time to fit residues: 377.8169 Evaluate side-chains 271 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 334 ARG Chi-restraints excluded: chain A residue 446 TRP Chi-restraints excluded: chain A residue 453 VAL 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 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 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 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 498 ILE 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 Chi-restraints excluded: chain C residue 793 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 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: 0.9182 ------------------------------------------------------------------------------- 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 C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095145 restraints weight = 12308.252| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.86 r_work: 0.2910 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9732 Z= 0.183 Angle : 0.541 9.104 13236 Z= 0.262 Chirality : 0.043 0.259 1574 Planarity : 0.003 0.034 1604 Dihedral : 6.466 50.426 1640 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 6.47 % Allowed : 23.14 % Favored : 70.39 % 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: 0.89 (0.24), residues: 1114 helix: 1.38 (0.23), residues: 490 sheet: 1.34 (0.29), residues: 270 loop : -1.13 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.003 0.001 HIS A 504 PHE 0.021 0.001 PHE A 312 TYR 0.025 0.001 TYR A 568 ARG 0.005 0.000 ARG C 523 *********************** 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 301 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 235 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8655 (mp10) cc_final: 0.7958 (mm-40) REVERT: A 207 GLU cc_start: 0.8978 (tt0) cc_final: 0.8774 (tt0) REVERT: A 256 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8441 (mp0) REVERT: A 265 LYS cc_start: 0.9356 (mttm) cc_final: 0.8997 (mtpt) REVERT: A 302 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7892 (mmmt) REVERT: A 306 TYR cc_start: 0.9104 (m-80) cc_final: 0.8825 (m-80) REVERT: A 334 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5575 (tpm170) REVERT: A 542 PHE cc_start: 0.8058 (m-10) cc_final: 0.7728 (m-10) REVERT: A 554 MET cc_start: 0.8649 (tpp) cc_final: 0.8216 (tpp) REVERT: A 559 SER cc_start: 0.8912 (m) cc_final: 0.8673 (t) REVERT: A 567 ASN cc_start: 0.8707 (t0) cc_final: 0.8442 (t160) REVERT: A 572 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8383 (mp10) REVERT: A 578 MET cc_start: 0.7502 (mmp) cc_final: 0.7135 (mmm) REVERT: A 608 PHE cc_start: 0.4900 (OUTLIER) cc_final: 0.3610 (m-80) REVERT: A 713 MET cc_start: 0.8855 (tpp) cc_final: 0.8571 (tpt) REVERT: A 718 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 732 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8111 (mppt) REVERT: A 737 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 774 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8820 (mt-10) REVERT: A 783 ILE cc_start: 0.8925 (pp) cc_final: 0.8565 (pp) REVERT: A 792 ASP cc_start: 0.9038 (m-30) cc_final: 0.8527 (m-30) REVERT: C 123 GLN cc_start: 0.8645 (mp10) cc_final: 0.7955 (mm-40) REVERT: C 207 GLU cc_start: 0.8975 (tt0) cc_final: 0.8772 (tt0) REVERT: C 256 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8418 (mp0) REVERT: C 265 LYS cc_start: 0.9351 (mttm) cc_final: 0.8995 (mtpt) REVERT: C 302 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7878 (mmmt) REVERT: C 306 TYR cc_start: 0.9109 (m-80) cc_final: 0.8830 (m-80) REVERT: C 334 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5573 (tpm170) REVERT: C 542 PHE cc_start: 0.8048 (m-10) cc_final: 0.7720 (m-10) REVERT: C 554 MET cc_start: 0.8636 (tpp) cc_final: 0.8209 (tpp) REVERT: C 559 SER cc_start: 0.8916 (m) cc_final: 0.8680 (t) REVERT: C 572 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8393 (mp10) REVERT: C 578 MET cc_start: 0.7510 (mmp) cc_final: 0.7142 (mmm) REVERT: C 608 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.3604 (m-80) REVERT: C 713 MET cc_start: 0.8857 (tpp) cc_final: 0.8566 (tpt) REVERT: C 718 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 732 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8110 (mppt) REVERT: C 737 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: C 774 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8838 (mt-10) REVERT: C 783 ILE cc_start: 0.8889 (pp) cc_final: 0.8523 (pp) REVERT: C 792 ASP cc_start: 0.9041 (m-30) cc_final: 0.8537 (m-30) outliers start: 66 outliers final: 29 residues processed: 277 average time/residue: 0.9007 time to fit residues: 272.4185 Evaluate side-chains 270 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 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 572 GLN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 718 ILE 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 758 LEU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 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 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 572 GLN Chi-restraints excluded: chain C residue 608 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 718 ILE 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 758 LEU 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: 0.8980 chunk 113 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 100 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 764 ASN C 467 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095036 restraints weight = 12307.972| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.83 r_work: 0.2923 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9732 Z= 0.196 Angle : 0.550 9.071 13236 Z= 0.271 Chirality : 0.044 0.257 1574 Planarity : 0.003 0.034 1604 Dihedral : 6.006 50.454 1640 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.20 % Allowed : 25.10 % 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: 1.49 (0.23), residues: 490 sheet: 1.35 (0.29), residues: 270 loop : -1.10 (0.29), 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 0.022 0.001 PHE A 312 TYR 0.022 0.001 TYR C 568 ARG 0.006 0.000 ARG A 518 *********************** 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 266 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8674 (mp10) cc_final: 0.8027 (mm-40) REVERT: A 207 GLU cc_start: 0.8993 (tt0) cc_final: 0.8786 (tt0) REVERT: A 256 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8435 (mp0) REVERT: A 265 LYS cc_start: 0.9355 (mttm) cc_final: 0.9034 (mtpt) REVERT: A 302 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7879 (mmmt) REVERT: A 306 TYR cc_start: 0.9063 (m-80) cc_final: 0.8744 (m-80) REVERT: A 334 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5541 (tpm170) REVERT: A 446 TRP cc_start: 0.8056 (t60) cc_final: 0.7761 (t-100) REVERT: A 542 PHE cc_start: 0.8014 (m-10) cc_final: 0.7692 (m-10) REVERT: A 554 MET cc_start: 0.8668 (tpp) cc_final: 0.8190 (tpp) REVERT: A 559 SER cc_start: 0.8909 (m) cc_final: 0.8674 (t) REVERT: A 572 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: A 578 MET cc_start: 0.7535 (mmp) cc_final: 0.7001 (mmm) REVERT: A 608 PHE cc_start: 0.4911 (OUTLIER) cc_final: 0.3625 (m-80) REVERT: A 713 MET cc_start: 0.8859 (tpp) cc_final: 0.8559 (tpt) REVERT: A 732 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8013 (mppt) REVERT: A 737 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 774 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8799 (mt-10) REVERT: A 783 ILE cc_start: 0.8950 (pp) cc_final: 0.8580 (pp) REVERT: A 792 ASP cc_start: 0.9041 (m-30) cc_final: 0.8536 (m-30) REVERT: C 123 GLN cc_start: 0.8670 (mp10) cc_final: 0.8030 (mm-40) REVERT: C 207 GLU cc_start: 0.8978 (tt0) cc_final: 0.8775 (tt0) REVERT: C 256 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8429 (mp0) REVERT: C 265 LYS cc_start: 0.9355 (mttm) cc_final: 0.9039 (mtpt) REVERT: C 302 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7868 (mmmt) REVERT: C 306 TYR cc_start: 0.9064 (m-80) cc_final: 0.8745 (m-80) REVERT: C 334 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5537 (tpm170) REVERT: C 446 TRP cc_start: 0.8051 (t60) cc_final: 0.7750 (t-100) REVERT: C 542 PHE cc_start: 0.8006 (m-10) cc_final: 0.7683 (m-10) REVERT: C 554 MET cc_start: 0.8657 (tpp) cc_final: 0.8181 (tpp) REVERT: C 559 SER cc_start: 0.8906 (m) cc_final: 0.8673 (t) REVERT: C 572 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: C 578 MET cc_start: 0.7540 (mmp) cc_final: 0.7004 (mmm) REVERT: C 608 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.3620 (m-80) REVERT: C 713 MET cc_start: 0.8853 (tpp) cc_final: 0.8558 (tpt) REVERT: C 732 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8012 (mppt) REVERT: C 737 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 774 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8826 (mt-10) REVERT: C 783 ILE cc_start: 0.8903 (pp) cc_final: 0.8488 (pp) REVERT: C 792 ASP cc_start: 0.9046 (m-30) cc_final: 0.8543 (m-30) outliers start: 53 outliers final: 29 residues processed: 247 average time/residue: 0.8360 time to fit residues: 226.9308 Evaluate side-chains 261 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 645 THR Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 764 ASN Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0670 chunk 42 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 C 475 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095222 restraints weight = 12367.026| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.84 r_work: 0.2929 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9732 Z= 0.191 Angle : 0.560 9.509 13236 Z= 0.272 Chirality : 0.044 0.253 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.724 50.490 1640 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 5.59 % Allowed : 24.80 % Favored : 69.61 % 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: 1.60 (0.22), residues: 502 sheet: 1.38 (0.29), residues: 270 loop : -1.13 (0.30), residues: 342 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 0.020 0.001 PHE A 312 TYR 0.025 0.001 TYR C 568 ARG 0.005 0.000 ARG C 518 *********************** 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 280 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8650 (mp10) cc_final: 0.8021 (mm-40) REVERT: A 256 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8444 (mp0) REVERT: A 265 LYS cc_start: 0.9353 (mttm) cc_final: 0.9030 (mtpt) REVERT: A 302 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7860 (mmmt) REVERT: A 306 TYR cc_start: 0.9048 (m-80) cc_final: 0.8703 (m-80) REVERT: A 334 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5534 (tpm170) REVERT: A 446 TRP cc_start: 0.8091 (t60) cc_final: 0.7808 (t-100) REVERT: A 542 PHE cc_start: 0.7989 (m-10) cc_final: 0.7676 (m-10) REVERT: A 554 MET cc_start: 0.8666 (tpp) cc_final: 0.8127 (tpp) REVERT: A 559 SER cc_start: 0.8901 (m) cc_final: 0.8674 (t) REVERT: A 572 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8514 (mp10) REVERT: A 578 MET cc_start: 0.7527 (mmp) cc_final: 0.7084 (mmm) REVERT: A 608 PHE cc_start: 0.5026 (OUTLIER) cc_final: 0.3678 (m-80) REVERT: A 713 MET cc_start: 0.8899 (tpp) cc_final: 0.8622 (tpt) REVERT: A 732 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8000 (mppt) REVERT: A 737 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: A 774 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8804 (mt-10) REVERT: A 783 ILE cc_start: 0.8967 (pp) cc_final: 0.8510 (pp) REVERT: A 792 ASP cc_start: 0.9042 (m-30) cc_final: 0.8526 (m-30) REVERT: C 123 GLN cc_start: 0.8642 (mp10) cc_final: 0.7999 (mm-40) REVERT: C 256 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8438 (mp0) REVERT: C 265 LYS cc_start: 0.9353 (mttm) cc_final: 0.9034 (mtpt) REVERT: C 302 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7850 (mmmt) REVERT: C 306 TYR cc_start: 0.9054 (m-80) cc_final: 0.8710 (m-80) REVERT: C 334 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5530 (tpm170) REVERT: C 446 TRP cc_start: 0.8091 (t60) cc_final: 0.7807 (t-100) REVERT: C 542 PHE cc_start: 0.7987 (m-10) cc_final: 0.7674 (m-10) REVERT: C 554 MET cc_start: 0.8653 (tpp) cc_final: 0.8115 (tpp) REVERT: C 559 SER cc_start: 0.8900 (m) cc_final: 0.8674 (t) REVERT: C 567 ASN cc_start: 0.8652 (t0) cc_final: 0.8369 (t160) REVERT: C 572 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: C 578 MET cc_start: 0.7524 (mmp) cc_final: 0.7081 (mmm) REVERT: C 608 PHE cc_start: 0.5024 (OUTLIER) cc_final: 0.3673 (m-80) REVERT: C 713 MET cc_start: 0.8898 (tpp) cc_final: 0.8621 (tpt) REVERT: C 732 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8002 (mppt) REVERT: C 737 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: C 774 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8829 (mt-10) REVERT: C 783 ILE cc_start: 0.8895 (pp) cc_final: 0.8540 (pp) REVERT: C 792 ASP cc_start: 0.9047 (m-30) cc_final: 0.8529 (m-30) outliers start: 57 outliers final: 31 residues processed: 262 average time/residue: 0.8802 time to fit residues: 252.8055 Evaluate side-chains 261 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 572 GLN 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 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 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 572 GLN 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: 4.9990 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 C 467 GLN C 475 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.143585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.095036 restraints weight = 12448.537| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.88 r_work: 0.2918 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9732 Z= 0.192 Angle : 0.553 9.693 13236 Z= 0.272 Chirality : 0.044 0.251 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.356 50.494 1640 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.71 % Allowed : 25.59 % 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: 1.23 (0.24), residues: 1114 helix: 1.75 (0.22), residues: 502 sheet: 1.39 (0.29), residues: 270 loop : -1.11 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.004 0.001 HIS C 504 PHE 0.019 0.001 PHE A 312 TYR 0.027 0.001 TYR A 568 ARG 0.005 0.000 ARG A 523 *********************** 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 279 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8612 (mp10) cc_final: 0.7945 (mm-40) REVERT: A 256 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8431 (mp0) REVERT: A 265 LYS cc_start: 0.9366 (mttm) cc_final: 0.9042 (mtpt) REVERT: A 302 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7827 (mmmt) REVERT: A 306 TYR cc_start: 0.9014 (m-80) cc_final: 0.8656 (m-80) REVERT: A 334 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5576 (tpm170) REVERT: A 446 TRP cc_start: 0.7934 (t60) cc_final: 0.7674 (t-100) REVERT: A 542 PHE cc_start: 0.7940 (m-10) cc_final: 0.7566 (m-10) REVERT: A 554 MET cc_start: 0.8655 (tpp) cc_final: 0.8106 (tpp) REVERT: A 608 PHE cc_start: 0.4962 (OUTLIER) cc_final: 0.3644 (m-80) REVERT: A 713 MET cc_start: 0.8844 (tpp) cc_final: 0.8560 (tpt) REVERT: A 732 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7982 (mppt) REVERT: A 737 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 774 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8784 (mt-10) REVERT: A 783 ILE cc_start: 0.8985 (pp) cc_final: 0.8554 (pp) REVERT: A 792 ASP cc_start: 0.9046 (m-30) cc_final: 0.8332 (m-30) REVERT: C 123 GLN cc_start: 0.8610 (mp10) cc_final: 0.7949 (mm-40) REVERT: C 256 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8376 (mp0) REVERT: C 265 LYS cc_start: 0.9365 (mttm) cc_final: 0.9040 (mtpt) REVERT: C 302 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7831 (mmmt) REVERT: C 306 TYR cc_start: 0.9014 (m-80) cc_final: 0.8652 (m-80) REVERT: C 334 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5567 (tpm170) REVERT: C 446 TRP cc_start: 0.7979 (t60) cc_final: 0.7681 (t-100) REVERT: C 542 PHE cc_start: 0.7942 (m-10) cc_final: 0.7562 (m-10) REVERT: C 554 MET cc_start: 0.8661 (tpp) cc_final: 0.8118 (tpp) REVERT: C 608 PHE cc_start: 0.4961 (OUTLIER) cc_final: 0.3646 (m-80) REVERT: C 713 MET cc_start: 0.8841 (tpp) cc_final: 0.8558 (tpt) REVERT: C 732 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7986 (mppt) REVERT: C 737 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 774 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 783 ILE cc_start: 0.8922 (pp) cc_final: 0.8556 (pp) REVERT: C 792 ASP cc_start: 0.9047 (m-30) cc_final: 0.8495 (m-30) outliers start: 48 outliers final: 30 residues processed: 265 average time/residue: 0.8724 time to fit residues: 253.8667 Evaluate side-chains 264 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 334 ARG Chi-restraints excluded: chain A residue 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 732 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain C residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.0370 chunk 90 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 467 GLN A 567 ASN C 467 GLN C 567 ASN 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 = 0.144050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095929 restraints weight = 12552.060| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.87 r_work: 0.2927 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9732 Z= 0.164 Angle : 0.551 9.762 13236 Z= 0.272 Chirality : 0.044 0.247 1574 Planarity : 0.003 0.035 1604 Dihedral : 5.137 50.656 1640 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.22 % Allowed : 26.76 % Favored : 69.02 % 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: 1.39 (0.24), residues: 1114 helix: 1.90 (0.23), residues: 502 sheet: 1.44 (0.29), residues: 270 loop : -1.04 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 106 HIS 0.005 0.001 HIS A 504 PHE 0.019 0.001 PHE A 312 TYR 0.027 0.001 TYR C 568 ARG 0.005 0.000 ARG C 523 ********************** 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 272 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.8587 (mp10) cc_final: 0.7990 (mm-40) REVERT: A 256 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8422 (mp0) REVERT: A 265 LYS cc_start: 0.9366 (mttm) cc_final: 0.9037 (mtpt) REVERT: A 306 TYR cc_start: 0.8983 (m-80) cc_final: 0.8630 (m-80) REVERT: A 446 TRP cc_start: 0.7968 (t60) cc_final: 0.7672 (t-100) REVERT: A 542 PHE cc_start: 0.7951 (m-10) cc_final: 0.7574 (m-10) REVERT: A 554 MET cc_start: 0.8662 (tpp) cc_final: 0.8104 (tpp) REVERT: A 608 PHE cc_start: 0.5200 (OUTLIER) cc_final: 0.3896 (m-80) REVERT: A 713 MET cc_start: 0.8827 (tpp) cc_final: 0.8557 (tpt) REVERT: A 732 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7995 (mppt) REVERT: A 737 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 774 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8787 (mt-10) REVERT: A 783 ILE cc_start: 0.8950 (pp) cc_final: 0.8475 (pp) REVERT: A 792 ASP cc_start: 0.9048 (m-30) cc_final: 0.8356 (m-30) REVERT: C 73 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8040 (p0) REVERT: C 123 GLN cc_start: 0.8596 (mp10) cc_final: 0.8002 (mm-40) REVERT: C 256 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8413 (mp0) REVERT: C 265 LYS cc_start: 0.9369 (mttm) cc_final: 0.9041 (mtpt) REVERT: C 306 TYR cc_start: 0.8982 (m-80) cc_final: 0.8628 (m-80) REVERT: C 446 TRP cc_start: 0.7985 (t60) cc_final: 0.7755 (t-100) REVERT: C 542 PHE cc_start: 0.7943 (m-10) cc_final: 0.7565 (m-10) REVERT: C 554 MET cc_start: 0.8663 (tpp) cc_final: 0.8109 (tpp) REVERT: C 608 PHE cc_start: 0.5199 (OUTLIER) cc_final: 0.3891 (m-80) REVERT: C 713 MET cc_start: 0.8828 (tpp) cc_final: 0.8555 (tpt) REVERT: C 732 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7995 (mppt) REVERT: C 737 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: C 763 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8407 (mm-40) REVERT: C 774 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 783 ILE cc_start: 0.8898 (pp) cc_final: 0.8530 (pp) REVERT: C 792 ASP cc_start: 0.9049 (m-30) cc_final: 0.8369 (m-30) outliers start: 43 outliers final: 28 residues processed: 261 average time/residue: 0.9287 time to fit residues: 266.1576 Evaluate side-chains 258 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 325 LEU 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 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 325 LEU 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 C 467 GLN C 567 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093073 restraints weight = 12493.983| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.85 r_work: 0.2892 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9732 Z= 0.340 Angle : 0.601 9.590 13236 Z= 0.301 Chirality : 0.046 0.268 1574 Planarity : 0.003 0.034 1604 Dihedral : 5.202 50.046 1640 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.12 % Allowed : 27.06 % Favored : 68.82 % 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: 1.27 (0.24), residues: 1114 helix: 1.85 (0.23), residues: 490 sheet: 1.31 (0.28), residues: 270 loop : -1.00 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 754 HIS 0.004 0.001 HIS A 504 PHE 0.032 0.001 PHE A 317 TYR 0.025 0.001 TYR A 568 ARG 0.005 0.000 ARG C 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7291.80 seconds wall clock time: 130 minutes 51.62 seconds (7851.62 seconds total)