Starting phenix.real_space_refine on Wed Jun 25 00:53:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ux1_26845/06_2025/7ux1_26845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ux1_26845/06_2025/7ux1_26845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ux1_26845/06_2025/7ux1_26845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ux1_26845/06_2025/7ux1_26845.map" model { file = "/net/cci-nas-00/data/ceres_data/7ux1_26845/06_2025/7ux1_26845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ux1_26845/06_2025/7ux1_26845.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 17857 2.51 5 N 5523 2.21 5 O 5530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28931 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "G" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "F" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "E" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "D" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "C" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "B" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Time building chain proxies: 20.95, per 1000 atoms: 0.72 Number of scatterers: 28931 At special positions: 0 Unit cell: (188.94, 187.06, 171.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 5530 8.00 N 5523 7.00 C 17857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 5.5 seconds 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9548 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 16 sheets defined 75.8% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 286 through 337 removed outlier: 3.541A pdb=" N GLU A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 4.134A pdb=" N ARG A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.882A pdb=" N GLU A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 Proline residue: A 480 - end of helix removed outlier: 4.282A pdb=" N LYS A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 536 Proline residue: A 512 - end of helix removed outlier: 4.106A pdb=" N TRP A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 575 Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Proline residue: A 639 - end of helix Processing helix chain 'A' and resid 660 through 684 removed outlier: 4.377A pdb=" N ILE A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) Proline residue: A 677 - end of helix Processing helix chain 'A' and resid 690 through 710 removed outlier: 4.117A pdb=" N VAL A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 695 " --> pdb=" O MET A 691 " (cutoff:3.500A) Proline residue: A 703 - end of helix removed outlier: 3.763A pdb=" N THR A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU A 719 " --> pdb=" O TYR A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'A' and resid 720 through 754 removed outlier: 4.139A pdb=" N ARG A 724 " --> pdb=" O ARG A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 811 removed outlier: 3.976A pdb=" N SER A 811 " --> pdb=" O TRP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 821 Processing helix chain 'A' and resid 842 through 873 removed outlier: 3.890A pdb=" N ARG A 861 " --> pdb=" O TRP A 857 " (cutoff:3.500A) Proline residue: A 864 - end of helix removed outlier: 3.905A pdb=" N LEU A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 906 Processing helix chain 'A' and resid 907 through 910 Processing helix chain 'A' and resid 914 through 944 removed outlier: 4.008A pdb=" N ALA A 918 " --> pdb=" O TRP A 914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 926 " --> pdb=" O GLY A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.983A pdb=" N PHE A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1062 No H-bonds generated for 'chain 'A' and resid 1060 through 1062' Processing helix chain 'A' and resid 1063 through 1083 Processing helix chain 'G' and resid 287 through 337 Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.134A pdb=" N ARG G 347 " --> pdb=" O LEU G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.882A pdb=" N GLU G 361 " --> pdb=" O SER G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 386 Processing helix chain 'G' and resid 388 through 398 Processing helix chain 'G' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 491 Proline residue: G 480 - end of helix removed outlier: 4.282A pdb=" N LYS G 484 " --> pdb=" O PRO G 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP G 485 " --> pdb=" O GLN G 481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS G 491 " --> pdb=" O PHE G 487 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 536 Proline residue: G 512 - end of helix removed outlier: 4.106A pdb=" N TRP G 522 " --> pdb=" O GLY G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 575 Proline residue: G 562 - end of helix Processing helix chain 'G' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER G 587 " --> pdb=" O GLU G 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE G 594 " --> pdb=" O LYS G 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS G 602 " --> pdb=" O VAL G 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP G 603 " --> pdb=" O PHE G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL G 631 " --> pdb=" O ARG G 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG G 632 " --> pdb=" O ARG G 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE G 633 " --> pdb=" O GLN G 629 " (cutoff:3.500A) Proline residue: G 639 - end of helix Processing helix chain 'G' and resid 660 through 684 removed outlier: 4.378A pdb=" N ILE G 664 " --> pdb=" O GLY G 660 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE G 666 " --> pdb=" O ALA G 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU G 669 " --> pdb=" O PHE G 665 " (cutoff:3.500A) Proline residue: G 677 - end of helix Processing helix chain 'G' and resid 690 through 710 removed outlier: 4.118A pdb=" N VAL G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR G 695 " --> pdb=" O MET G 691 " (cutoff:3.500A) Proline residue: G 703 - end of helix removed outlier: 3.763A pdb=" N THR G 710 " --> pdb=" O LEU G 706 " (cutoff:3.500A) Processing helix chain 'G' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU G 719 " --> pdb=" O TYR G 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 716 through 719' Processing helix chain 'G' and resid 720 through 754 removed outlier: 4.139A pdb=" N ARG G 724 " --> pdb=" O ARG G 720 " (cutoff:3.500A) Processing helix chain 'G' and resid 788 through 811 removed outlier: 3.976A pdb=" N SER G 811 " --> pdb=" O TRP G 807 " (cutoff:3.500A) Processing helix chain 'G' and resid 812 through 821 Processing helix chain 'G' and resid 842 through 873 removed outlier: 3.889A pdb=" N ARG G 861 " --> pdb=" O TRP G 857 " (cutoff:3.500A) Proline residue: G 864 - end of helix removed outlier: 3.905A pdb=" N LEU G 870 " --> pdb=" O LEU G 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER G 873 " --> pdb=" O VAL G 869 " (cutoff:3.500A) Processing helix chain 'G' and resid 880 through 906 Processing helix chain 'G' and resid 907 through 910 Processing helix chain 'G' and resid 914 through 944 removed outlier: 4.008A pdb=" N ALA G 918 " --> pdb=" O TRP G 914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY G 926 " --> pdb=" O GLY G 922 " (cutoff:3.500A) Processing helix chain 'G' and resid 982 through 989 removed outlier: 3.983A pdb=" N PHE G 986 " --> pdb=" O PRO G 982 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL G 987 " --> pdb=" O ASN G 983 " (cutoff:3.500A) Processing helix chain 'G' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA G1025 " --> pdb=" O VAL G1021 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G1026 " --> pdb=" O LEU G1022 " (cutoff:3.500A) Processing helix chain 'G' and resid 1060 through 1062 No H-bonds generated for 'chain 'G' and resid 1060 through 1062' Processing helix chain 'G' and resid 1063 through 1083 Processing helix chain 'F' and resid 287 through 337 Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.135A pdb=" N ARG F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 362 removed outlier: 3.881A pdb=" N GLU F 361 " --> pdb=" O SER F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 386 Processing helix chain 'F' and resid 388 through 398 Processing helix chain 'F' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 491 Proline residue: F 480 - end of helix removed outlier: 4.282A pdb=" N LYS F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP F 485 " --> pdb=" O GLN F 481 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS F 491 " --> pdb=" O PHE F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 536 Proline residue: F 512 - end of helix removed outlier: 4.106A pdb=" N TRP F 522 " --> pdb=" O GLY F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 575 Proline residue: F 562 - end of helix Processing helix chain 'F' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER F 587 " --> pdb=" O GLU F 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE F 594 " --> pdb=" O LYS F 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS F 602 " --> pdb=" O VAL F 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP F 603 " --> pdb=" O PHE F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL F 631 " --> pdb=" O ARG F 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG F 632 " --> pdb=" O ARG F 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE F 633 " --> pdb=" O GLN F 629 " (cutoff:3.500A) Proline residue: F 639 - end of helix Processing helix chain 'F' and resid 660 through 684 removed outlier: 4.378A pdb=" N ILE F 664 " --> pdb=" O GLY F 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE F 666 " --> pdb=" O ALA F 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 669 " --> pdb=" O PHE F 665 " (cutoff:3.500A) Proline residue: F 677 - end of helix Processing helix chain 'F' and resid 690 through 710 removed outlier: 4.117A pdb=" N VAL F 694 " --> pdb=" O THR F 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR F 695 " --> pdb=" O MET F 691 " (cutoff:3.500A) Proline residue: F 703 - end of helix removed outlier: 3.764A pdb=" N THR F 710 " --> pdb=" O LEU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU F 719 " --> pdb=" O TYR F 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 716 through 719' Processing helix chain 'F' and resid 720 through 754 removed outlier: 4.139A pdb=" N ARG F 724 " --> pdb=" O ARG F 720 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 811 removed outlier: 3.976A pdb=" N SER F 811 " --> pdb=" O TRP F 807 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 821 Processing helix chain 'F' and resid 842 through 873 removed outlier: 3.889A pdb=" N ARG F 861 " --> pdb=" O TRP F 857 " (cutoff:3.500A) Proline residue: F 864 - end of helix removed outlier: 3.905A pdb=" N LEU F 870 " --> pdb=" O LEU F 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER F 873 " --> pdb=" O VAL F 869 " (cutoff:3.500A) Processing helix chain 'F' and resid 880 through 906 Processing helix chain 'F' and resid 907 through 910 Processing helix chain 'F' and resid 914 through 944 removed outlier: 4.008A pdb=" N ALA F 918 " --> pdb=" O TRP F 914 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY F 926 " --> pdb=" O GLY F 922 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 989 removed outlier: 3.984A pdb=" N PHE F 986 " --> pdb=" O PRO F 982 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL F 987 " --> pdb=" O ASN F 983 " (cutoff:3.500A) Processing helix chain 'F' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA F1025 " --> pdb=" O VAL F1021 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F1026 " --> pdb=" O LEU F1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 1060 through 1062 No H-bonds generated for 'chain 'F' and resid 1060 through 1062' Processing helix chain 'F' and resid 1063 through 1083 Processing helix chain 'E' and resid 287 through 337 Processing helix chain 'E' and resid 343 through 356 removed outlier: 4.134A pdb=" N ARG E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 362 removed outlier: 3.882A pdb=" N GLU E 361 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 386 Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 491 Proline residue: E 480 - end of helix removed outlier: 4.282A pdb=" N LYS E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP E 485 " --> pdb=" O GLN E 481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS E 491 " --> pdb=" O PHE E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 536 Proline residue: E 512 - end of helix removed outlier: 4.106A pdb=" N TRP E 522 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 575 Proline residue: E 562 - end of helix Processing helix chain 'E' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER E 587 " --> pdb=" O GLU E 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE E 594 " --> pdb=" O LYS E 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS E 602 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 603 " --> pdb=" O PHE E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL E 631 " --> pdb=" O ARG E 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG E 632 " --> pdb=" O ARG E 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 633 " --> pdb=" O GLN E 629 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'E' and resid 660 through 684 removed outlier: 4.378A pdb=" N ILE E 664 " --> pdb=" O GLY E 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE E 666 " --> pdb=" O ALA E 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 669 " --> pdb=" O PHE E 665 " (cutoff:3.500A) Proline residue: E 677 - end of helix Processing helix chain 'E' and resid 690 through 710 removed outlier: 4.117A pdb=" N VAL E 694 " --> pdb=" O THR E 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR E 695 " --> pdb=" O MET E 691 " (cutoff:3.500A) Proline residue: E 703 - end of helix removed outlier: 3.764A pdb=" N THR E 710 " --> pdb=" O LEU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU E 719 " --> pdb=" O TYR E 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 716 through 719' Processing helix chain 'E' and resid 720 through 754 removed outlier: 4.139A pdb=" N ARG E 724 " --> pdb=" O ARG E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 811 removed outlier: 3.976A pdb=" N SER E 811 " --> pdb=" O TRP E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 821 Processing helix chain 'E' and resid 842 through 873 removed outlier: 3.889A pdb=" N ARG E 861 " --> pdb=" O TRP E 857 " (cutoff:3.500A) Proline residue: E 864 - end of helix removed outlier: 3.905A pdb=" N LEU E 870 " --> pdb=" O LEU E 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 873 " --> pdb=" O VAL E 869 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 906 Processing helix chain 'E' and resid 907 through 910 Processing helix chain 'E' and resid 914 through 944 removed outlier: 4.009A pdb=" N ALA E 918 " --> pdb=" O TRP E 914 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 926 " --> pdb=" O GLY E 922 " (cutoff:3.500A) Processing helix chain 'E' and resid 982 through 989 removed outlier: 3.983A pdb=" N PHE E 986 " --> pdb=" O PRO E 982 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL E 987 " --> pdb=" O ASN E 983 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA E1025 " --> pdb=" O VAL E1021 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E1026 " --> pdb=" O LEU E1022 " (cutoff:3.500A) Processing helix chain 'E' and resid 1060 through 1062 No H-bonds generated for 'chain 'E' and resid 1060 through 1062' Processing helix chain 'E' and resid 1063 through 1083 Processing helix chain 'D' and resid 287 through 337 Processing helix chain 'D' and resid 343 through 356 removed outlier: 4.134A pdb=" N ARG D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 362 removed outlier: 3.882A pdb=" N GLU D 361 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 388 through 398 Processing helix chain 'D' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 Proline residue: D 480 - end of helix removed outlier: 4.282A pdb=" N LYS D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP D 485 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 536 Proline residue: D 512 - end of helix removed outlier: 4.106A pdb=" N TRP D 522 " --> pdb=" O GLY D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 575 Proline residue: D 562 - end of helix Processing helix chain 'D' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 603 " --> pdb=" O PHE D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL D 631 " --> pdb=" O ARG D 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG D 632 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) Proline residue: D 639 - end of helix Processing helix chain 'D' and resid 660 through 684 removed outlier: 4.378A pdb=" N ILE D 664 " --> pdb=" O GLY D 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 669 " --> pdb=" O PHE D 665 " (cutoff:3.500A) Proline residue: D 677 - end of helix Processing helix chain 'D' and resid 690 through 710 removed outlier: 4.118A pdb=" N VAL D 694 " --> pdb=" O THR D 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR D 695 " --> pdb=" O MET D 691 " (cutoff:3.500A) Proline residue: D 703 - end of helix removed outlier: 3.764A pdb=" N THR D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU D 719 " --> pdb=" O TYR D 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 716 through 719' Processing helix chain 'D' and resid 720 through 754 removed outlier: 4.139A pdb=" N ARG D 724 " --> pdb=" O ARG D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 811 removed outlier: 3.977A pdb=" N SER D 811 " --> pdb=" O TRP D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 821 Processing helix chain 'D' and resid 842 through 873 removed outlier: 3.889A pdb=" N ARG D 861 " --> pdb=" O TRP D 857 " (cutoff:3.500A) Proline residue: D 864 - end of helix removed outlier: 3.906A pdb=" N LEU D 870 " --> pdb=" O LEU D 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER D 873 " --> pdb=" O VAL D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 906 Processing helix chain 'D' and resid 907 through 910 Processing helix chain 'D' and resid 914 through 944 removed outlier: 4.009A pdb=" N ALA D 918 " --> pdb=" O TRP D 914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 926 " --> pdb=" O GLY D 922 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 989 removed outlier: 3.983A pdb=" N PHE D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA D1025 " --> pdb=" O VAL D1021 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D1026 " --> pdb=" O LEU D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1062 No H-bonds generated for 'chain 'D' and resid 1060 through 1062' Processing helix chain 'D' and resid 1063 through 1083 Processing helix chain 'C' and resid 287 through 337 Processing helix chain 'C' and resid 343 through 356 removed outlier: 4.134A pdb=" N ARG C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.882A pdb=" N GLU C 361 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 386 Processing helix chain 'C' and resid 388 through 398 Processing helix chain 'C' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 491 Proline residue: C 480 - end of helix removed outlier: 4.282A pdb=" N LYS C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 485 " --> pdb=" O GLN C 481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 536 Proline residue: C 512 - end of helix removed outlier: 4.106A pdb=" N TRP C 522 " --> pdb=" O GLY C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 575 Proline residue: C 562 - end of helix Processing helix chain 'C' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE C 594 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP C 603 " --> pdb=" O PHE C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL C 631 " --> pdb=" O ARG C 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG C 632 " --> pdb=" O ARG C 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) Proline residue: C 639 - end of helix Processing helix chain 'C' and resid 660 through 684 removed outlier: 4.378A pdb=" N ILE C 664 " --> pdb=" O GLY C 660 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 666 " --> pdb=" O ALA C 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) Proline residue: C 677 - end of helix Processing helix chain 'C' and resid 690 through 710 removed outlier: 4.118A pdb=" N VAL C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR C 695 " --> pdb=" O MET C 691 " (cutoff:3.500A) Proline residue: C 703 - end of helix removed outlier: 3.764A pdb=" N THR C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU C 719 " --> pdb=" O TYR C 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 716 through 719' Processing helix chain 'C' and resid 720 through 754 removed outlier: 4.139A pdb=" N ARG C 724 " --> pdb=" O ARG C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 811 removed outlier: 3.976A pdb=" N SER C 811 " --> pdb=" O TRP C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 821 Processing helix chain 'C' and resid 842 through 873 removed outlier: 3.890A pdb=" N ARG C 861 " --> pdb=" O TRP C 857 " (cutoff:3.500A) Proline residue: C 864 - end of helix removed outlier: 3.906A pdb=" N LEU C 870 " --> pdb=" O LEU C 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 873 " --> pdb=" O VAL C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 906 Processing helix chain 'C' and resid 907 through 910 Processing helix chain 'C' and resid 914 through 944 removed outlier: 4.009A pdb=" N ALA C 918 " --> pdb=" O TRP C 914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 926 " --> pdb=" O GLY C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 989 removed outlier: 3.984A pdb=" N PHE C 986 " --> pdb=" O PRO C 982 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA C1025 " --> pdb=" O VAL C1021 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1062 No H-bonds generated for 'chain 'C' and resid 1060 through 1062' Processing helix chain 'C' and resid 1063 through 1083 Processing helix chain 'B' and resid 287 through 337 Processing helix chain 'B' and resid 343 through 356 removed outlier: 4.135A pdb=" N ARG B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.881A pdb=" N GLU B 361 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 386 Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 405 through 464 removed outlier: 4.593A pdb=" N TRP B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 491 Proline residue: B 480 - end of helix removed outlier: 4.282A pdb=" N LYS B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 536 Proline residue: B 512 - end of helix removed outlier: 4.106A pdb=" N TRP B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 575 Proline residue: B 562 - end of helix Processing helix chain 'B' and resid 583 through 604 removed outlier: 3.622A pdb=" N SER B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 645 removed outlier: 5.015A pdb=" N VAL B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ARG B 632 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) Proline residue: B 639 - end of helix Processing helix chain 'B' and resid 660 through 684 removed outlier: 4.377A pdb=" N ILE B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Proline residue: B 677 - end of helix Processing helix chain 'B' and resid 690 through 710 removed outlier: 4.117A pdb=" N VAL B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 695 " --> pdb=" O MET B 691 " (cutoff:3.500A) Proline residue: B 703 - end of helix removed outlier: 3.763A pdb=" N THR B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 719 removed outlier: 4.278A pdb=" N LEU B 719 " --> pdb=" O TYR B 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 716 through 719' Processing helix chain 'B' and resid 720 through 754 removed outlier: 4.138A pdb=" N ARG B 724 " --> pdb=" O ARG B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 811 removed outlier: 3.976A pdb=" N SER B 811 " --> pdb=" O TRP B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 821 Processing helix chain 'B' and resid 842 through 873 removed outlier: 3.890A pdb=" N ARG B 861 " --> pdb=" O TRP B 857 " (cutoff:3.500A) Proline residue: B 864 - end of helix removed outlier: 3.906A pdb=" N LEU B 870 " --> pdb=" O LEU B 866 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 906 Processing helix chain 'B' and resid 907 through 910 Processing helix chain 'B' and resid 914 through 944 removed outlier: 4.008A pdb=" N ALA B 918 " --> pdb=" O TRP B 914 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 926 " --> pdb=" O GLY B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 989 removed outlier: 3.983A pdb=" N PHE B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1028 removed outlier: 3.581A pdb=" N ALA B1025 " --> pdb=" O VAL B1021 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1062 No H-bonds generated for 'chain 'B' and resid 1060 through 1062' Processing helix chain 'B' and resid 1063 through 1083 Processing sheet with id=AA1, first strand: chain 'A' and resid 827 through 832 Processing sheet with id=AA2, first strand: chain 'A' and resid 951 through 953 removed outlier: 6.463A pdb=" N THR A 970 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 991 " --> pdb=" O ILE A 980 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR G 970 " --> pdb=" O SER G 962 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 991 " --> pdb=" O ILE G 980 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR F 970 " --> pdb=" O SER F 962 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E 991 " --> pdb=" O ILE F 980 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR E 970 " --> pdb=" O SER E 962 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 991 " --> pdb=" O ILE E 980 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 970 " --> pdb=" O SER D 962 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 991 " --> pdb=" O ILE D 980 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C 970 " --> pdb=" O SER C 962 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 991 " --> pdb=" O ILE C 980 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 970 " --> pdb=" O SER B 962 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 991 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1001 through 1009 removed outlier: 6.912A pdb=" N ASP A1051 " --> pdb=" O THR A1043 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1090 through 1096 removed outlier: 3.523A pdb=" N HIS G1094 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A1093 " --> pdb=" O HIS G1094 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G1093 " --> pdb=" O HIS F1094 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F1093 " --> pdb=" O HIS E1094 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E1093 " --> pdb=" O HIS D1094 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D1093 " --> pdb=" O HIS C1094 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C1093 " --> pdb=" O HIS B1094 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N LEU B1091 " --> pdb=" O GLN A1090 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU A1092 " --> pdb=" O LEU B1091 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B1093 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N HIS A1094 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B1095 " --> pdb=" O HIS A1094 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS A1096 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 827 through 832 Processing sheet with id=AA6, first strand: chain 'G' and resid 1001 through 1009 removed outlier: 6.911A pdb=" N ASP G1051 " --> pdb=" O THR G1043 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 827 through 832 Processing sheet with id=AA8, first strand: chain 'F' and resid 1001 through 1009 removed outlier: 6.911A pdb=" N ASP F1051 " --> pdb=" O THR F1043 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 827 through 832 Processing sheet with id=AB1, first strand: chain 'E' and resid 1001 through 1009 removed outlier: 6.911A pdb=" N ASP E1051 " --> pdb=" O THR E1043 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 827 through 832 Processing sheet with id=AB3, first strand: chain 'D' and resid 1001 through 1009 removed outlier: 6.911A pdb=" N ASP D1051 " --> pdb=" O THR D1043 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 827 through 832 Processing sheet with id=AB5, first strand: chain 'C' and resid 1001 through 1009 removed outlier: 6.911A pdb=" N ASP C1051 " --> pdb=" O THR C1043 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 827 through 832 Processing sheet with id=AB7, first strand: chain 'B' and resid 1001 through 1009 removed outlier: 6.911A pdb=" N ASP B1051 " --> pdb=" O THR B1043 " (cutoff:3.500A) 3005 hydrogen bonds defined for protein. 8847 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: 11.52 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6237 1.33 - 1.45: 5715 1.45 - 1.57: 17112 1.57 - 1.68: 0 1.68 - 1.80: 35 Bond restraints: 29099 Sorted by residual: bond pdb=" CA ASP F1014 " pdb=" C ASP F1014 " ideal model delta sigma weight residual 1.527 1.498 0.029 1.35e-02 5.49e+03 4.52e+00 bond pdb=" CA ASP D1014 " pdb=" C ASP D1014 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.32e-02 5.74e+03 3.86e+00 bond pdb=" CA ASP A1014 " pdb=" C ASP A1014 " ideal model delta sigma weight residual 1.527 1.500 0.026 1.35e-02 5.49e+03 3.79e+00 bond pdb=" CA ASP G1014 " pdb=" C ASP G1014 " ideal model delta sigma weight residual 1.527 1.501 0.026 1.35e-02 5.49e+03 3.64e+00 bond pdb=" C ASP B1014 " pdb=" O ASP B1014 " ideal model delta sigma weight residual 1.234 1.211 0.023 1.27e-02 6.20e+03 3.20e+00 ... (remaining 29094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 39476 1.90 - 3.79: 586 3.79 - 5.69: 39 5.69 - 7.59: 23 7.59 - 9.48: 7 Bond angle restraints: 40131 Sorted by residual: angle pdb=" N PHE C1045 " pdb=" CA PHE C1045 " pdb=" C PHE C1045 " ideal model delta sigma weight residual 108.41 100.93 7.48 1.61e+00 3.86e-01 2.16e+01 angle pdb=" N PHE G1045 " pdb=" CA PHE G1045 " pdb=" C PHE G1045 " ideal model delta sigma weight residual 108.41 100.97 7.44 1.61e+00 3.86e-01 2.14e+01 angle pdb=" N PHE E1045 " pdb=" CA PHE E1045 " pdb=" C PHE E1045 " ideal model delta sigma weight residual 108.41 100.99 7.42 1.61e+00 3.86e-01 2.12e+01 angle pdb=" N TYR G1011 " pdb=" CA TYR G1011 " pdb=" C TYR G1011 " ideal model delta sigma weight residual 111.28 116.26 -4.98 1.09e+00 8.42e-01 2.08e+01 angle pdb=" N TYR D1011 " pdb=" CA TYR D1011 " pdb=" C TYR D1011 " ideal model delta sigma weight residual 111.28 116.23 -4.95 1.09e+00 8.42e-01 2.06e+01 ... (remaining 40126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16131 17.93 - 35.85: 777 35.85 - 53.78: 193 53.78 - 71.71: 14 71.71 - 89.64: 14 Dihedral angle restraints: 17129 sinusoidal: 2625 harmonic: 14504 Sorted by residual: dihedral pdb=" CA GLU E1035 " pdb=" C GLU E1035 " pdb=" N PRO E1036 " pdb=" CA PRO E1036 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLU A1035 " pdb=" C GLU A1035 " pdb=" N PRO A1036 " pdb=" CA PRO A1036 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA GLU F1035 " pdb=" C GLU F1035 " pdb=" N PRO F1036 " pdb=" CA PRO F1036 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 17126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4144 0.044 - 0.089: 964 0.089 - 0.133: 226 0.133 - 0.178: 14 0.178 - 0.222: 14 Chirality restraints: 5362 Sorted by residual: chirality pdb=" CB THR D 886 " pdb=" CA THR D 886 " pdb=" OG1 THR D 886 " pdb=" CG2 THR D 886 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR B 886 " pdb=" CA THR B 886 " pdb=" OG1 THR B 886 " pdb=" CG2 THR B 886 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR A 886 " pdb=" CA THR A 886 " pdb=" OG1 THR A 886 " pdb=" CG2 THR A 886 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 5359 not shown) Planarity restraints: 5432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C1013 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.06e+00 pdb=" C SER C1013 " -0.035 2.00e-02 2.50e+03 pdb=" O SER C1013 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP C1014 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 863 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.69e+00 pdb=" N PRO A 864 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 863 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 864 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 864 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 864 " -0.027 5.00e-02 4.00e+02 ... (remaining 5429 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6917 2.79 - 3.32: 30781 3.32 - 3.84: 48169 3.84 - 4.37: 43924 4.37 - 4.90: 80605 Nonbonded interactions: 210396 Sorted by model distance: nonbonded pdb=" O SER B 956 " pdb=" OG SER B 956 " model vdw 2.260 3.040 nonbonded pdb=" O SER G 956 " pdb=" OG SER G 956 " model vdw 2.261 3.040 nonbonded pdb=" O SER D 956 " pdb=" OG SER D 956 " model vdw 2.261 3.040 nonbonded pdb=" O SER C 956 " pdb=" OG SER C 956 " model vdw 2.261 3.040 nonbonded pdb=" O SER E 956 " pdb=" OG SER E 956 " model vdw 2.261 3.040 ... (remaining 210391 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: 0.29 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 38.160 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: 0.060 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 74.680 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29099 Z= 0.160 Angle : 0.560 9.482 40131 Z= 0.344 Chirality : 0.041 0.222 5362 Planarity : 0.003 0.048 5432 Dihedral : 12.464 89.636 7581 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 29.79 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.13), residues: 4865 helix: 3.23 (0.08), residues: 3556 sheet: -0.34 (0.29), residues: 357 loop : -1.56 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 857 HIS 0.002 0.001 HIS C1052 PHE 0.006 0.001 PHE D1042 TYR 0.006 0.001 TYR F1011 ARG 0.005 0.001 ARG C 944 Details of bonding type rmsd hydrogen bonds : bond 0.11407 ( 3005) hydrogen bonds : angle 3.99676 ( 8847) covalent geometry : bond 0.00275 (29099) covalent geometry : angle 0.55975 (40131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 2.814 Fit side-chains REVERT: A 889 LEU cc_start: 0.8173 (mt) cc_final: 0.7884 (mt) REVERT: A 1076 ASP cc_start: 0.8351 (t0) cc_final: 0.8027 (t0) REVERT: G 892 ILE cc_start: 0.8580 (mm) cc_final: 0.8379 (mm) REVERT: G 893 ILE cc_start: 0.8820 (mm) cc_final: 0.8590 (mm) REVERT: G 984 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8609 (mtmm) REVERT: G 1063 ASP cc_start: 0.7325 (t70) cc_final: 0.7089 (t0) REVERT: G 1080 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7682 (ptp-170) REVERT: F 1031 ARG cc_start: 0.7503 (mmm160) cc_final: 0.6889 (mmm160) REVERT: F 1063 ASP cc_start: 0.7285 (t70) cc_final: 0.6328 (t0) REVERT: F 1076 ASP cc_start: 0.8596 (t0) cc_final: 0.8334 (t0) REVERT: E 889 LEU cc_start: 0.8090 (mt) cc_final: 0.7742 (mt) REVERT: E 891 TYR cc_start: 0.8159 (m-80) cc_final: 0.7656 (m-80) REVERT: E 944 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.8035 (mtp85) REVERT: E 995 SER cc_start: 0.7906 (t) cc_final: 0.7697 (p) REVERT: E 1076 ASP cc_start: 0.8451 (t0) cc_final: 0.8130 (t0) REVERT: D 889 LEU cc_start: 0.8081 (mt) cc_final: 0.7805 (mt) REVERT: C 888 ILE cc_start: 0.8051 (mm) cc_final: 0.7840 (mm) REVERT: C 889 LEU cc_start: 0.8135 (mt) cc_final: 0.7852 (mt) REVERT: C 892 ILE cc_start: 0.8597 (mm) cc_final: 0.8393 (mm) REVERT: C 1051 ASP cc_start: 0.7825 (t0) cc_final: 0.7620 (t0) REVERT: B 891 TYR cc_start: 0.8007 (m-80) cc_final: 0.7647 (m-80) REVERT: B 984 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8330 (mtmm) REVERT: B 1053 GLU cc_start: 0.8214 (tt0) cc_final: 0.7922 (tt0) REVERT: B 1080 ARG cc_start: 0.8199 (ptp-170) cc_final: 0.7907 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 563 average time/residue: 0.4573 time to fit residues: 413.9136 Evaluate side-chains 543 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 0.9980 chunk 376 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 254 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 389 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 236 optimal weight: 20.0000 chunk 289 optimal weight: 0.0570 chunk 451 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1096 HIS G1096 HIS F 933 ASN F1082 ASN F1096 HIS E1096 HIS D1096 HIS C1096 HIS B1082 ASN B1096 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.193877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.144026 restraints weight = 56340.002| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.19 r_work: 0.3590 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 29099 Z= 0.129 Angle : 0.445 8.359 40131 Z= 0.246 Chirality : 0.039 0.155 5362 Planarity : 0.003 0.043 5432 Dihedral : 3.642 22.689 5068 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.14 % Allowed : 28.98 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.13), residues: 4865 helix: 3.37 (0.08), residues: 3584 sheet: -0.13 (0.29), residues: 343 loop : -1.79 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 857 HIS 0.005 0.001 HIS B1096 PHE 0.013 0.001 PHE D1045 TYR 0.007 0.001 TYR B 891 ARG 0.007 0.001 ARG E1031 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 3005) hydrogen bonds : angle 3.37243 ( 8847) covalent geometry : bond 0.00262 (29099) covalent geometry : angle 0.44455 (40131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 550 time to evaluate : 2.918 Fit side-chains REVERT: A 889 LEU cc_start: 0.8256 (mt) cc_final: 0.7930 (mt) REVERT: A 944 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8183 (mtp-110) REVERT: A 995 SER cc_start: 0.8230 (t) cc_final: 0.7929 (p) REVERT: A 1063 ASP cc_start: 0.7069 (t0) cc_final: 0.6813 (t0) REVERT: A 1079 CYS cc_start: 0.8344 (t) cc_final: 0.8009 (m) REVERT: G 889 LEU cc_start: 0.8103 (mt) cc_final: 0.7621 (mt) REVERT: G 893 ILE cc_start: 0.8827 (mm) cc_final: 0.8620 (mm) REVERT: G 995 SER cc_start: 0.8272 (t) cc_final: 0.7973 (p) REVERT: G 1063 ASP cc_start: 0.7004 (t70) cc_final: 0.6800 (t0) REVERT: F 1031 ARG cc_start: 0.7413 (mmm160) cc_final: 0.6721 (mmm160) REVERT: F 1063 ASP cc_start: 0.7146 (t70) cc_final: 0.6202 (t0) REVERT: F 1066 ARG cc_start: 0.7776 (mmm160) cc_final: 0.7496 (mmp80) REVERT: F 1076 ASP cc_start: 0.8618 (t0) cc_final: 0.8252 (t0) REVERT: F 1079 CYS cc_start: 0.8066 (t) cc_final: 0.7796 (m) REVERT: F 1093 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8523 (m) REVERT: E 889 LEU cc_start: 0.8154 (mt) cc_final: 0.7812 (mt) REVERT: E 890 ASN cc_start: 0.8694 (m-40) cc_final: 0.8471 (t0) REVERT: E 995 SER cc_start: 0.8089 (t) cc_final: 0.7813 (p) REVERT: E 1031 ARG cc_start: 0.7346 (mmm160) cc_final: 0.7052 (mmm-85) REVERT: E 1063 ASP cc_start: 0.7159 (t0) cc_final: 0.6931 (t0) REVERT: E 1076 ASP cc_start: 0.8394 (t0) cc_final: 0.8092 (t0) REVERT: D 889 LEU cc_start: 0.8190 (mt) cc_final: 0.7847 (mt) REVERT: D 893 ILE cc_start: 0.8596 (mm) cc_final: 0.8385 (mm) REVERT: D 1063 ASP cc_start: 0.7211 (t70) cc_final: 0.6986 (t70) REVERT: C 889 LEU cc_start: 0.8219 (mt) cc_final: 0.7951 (mt) REVERT: C 892 ILE cc_start: 0.8603 (mm) cc_final: 0.8368 (mm) REVERT: C 970 THR cc_start: 0.8783 (p) cc_final: 0.8537 (m) REVERT: C 1053 GLU cc_start: 0.8248 (tt0) cc_final: 0.7957 (tt0) REVERT: C 1063 ASP cc_start: 0.7191 (t0) cc_final: 0.6904 (t0) REVERT: C 1079 CYS cc_start: 0.8204 (t) cc_final: 0.7964 (m) REVERT: B 891 TYR cc_start: 0.8069 (m-80) cc_final: 0.7747 (m-80) REVERT: B 927 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.7048 (mp) REVERT: B 984 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8457 (mtmm) REVERT: B 995 SER cc_start: 0.8452 (t) cc_final: 0.8182 (p) REVERT: B 1063 ASP cc_start: 0.7083 (t0) cc_final: 0.6746 (t0) outliers start: 51 outliers final: 35 residues processed: 581 average time/residue: 0.3761 time to fit residues: 351.9977 Evaluate side-chains 580 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 543 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 894 ILE Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1093 VAL Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 953 THR Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 896 VAL Chi-restraints excluded: chain D residue 902 PHE Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1004 VAL Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1096 HIS Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 116 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 chunk 490 optimal weight: 0.4980 chunk 376 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 338 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1096 HIS F 933 ASN F1052 HIS F1096 HIS E1096 HIS D1096 HIS C1096 HIS B1082 ASN B1096 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.190424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145419 restraints weight = 56188.750| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 5.18 r_work: 0.3481 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29099 Z= 0.274 Angle : 0.539 9.778 40131 Z= 0.306 Chirality : 0.042 0.164 5362 Planarity : 0.004 0.061 5432 Dihedral : 4.017 24.349 5068 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.25 % Allowed : 28.57 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.12), residues: 4865 helix: 3.16 (0.08), residues: 3570 sheet: -0.29 (0.30), residues: 336 loop : -1.93 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 994 HIS 0.014 0.003 HIS C1096 PHE 0.029 0.002 PHE D1042 TYR 0.012 0.002 TYR E1011 ARG 0.009 0.001 ARG B1031 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 3005) hydrogen bonds : angle 3.69235 ( 8847) covalent geometry : bond 0.00600 (29099) covalent geometry : angle 0.53896 (40131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 543 time to evaluate : 2.834 Fit side-chains REVERT: A 889 LEU cc_start: 0.8314 (mt) cc_final: 0.7971 (mt) REVERT: A 944 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8234 (mtp180) REVERT: A 995 SER cc_start: 0.8372 (t) cc_final: 0.8097 (p) REVERT: A 1063 ASP cc_start: 0.7353 (t0) cc_final: 0.6970 (t0) REVERT: G 925 PHE cc_start: 0.7687 (t80) cc_final: 0.7369 (t80) REVERT: G 1063 ASP cc_start: 0.7421 (t70) cc_final: 0.7188 (t0) REVERT: G 1079 CYS cc_start: 0.8017 (t) cc_final: 0.7732 (m) REVERT: F 914 TRP cc_start: 0.6905 (m100) cc_final: 0.6653 (m-10) REVERT: F 1063 ASP cc_start: 0.7501 (t70) cc_final: 0.7300 (t0) REVERT: F 1066 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7703 (mmp80) REVERT: F 1076 ASP cc_start: 0.8483 (t0) cc_final: 0.8182 (t0) REVERT: F 1079 CYS cc_start: 0.8088 (t) cc_final: 0.7849 (m) REVERT: E 889 LEU cc_start: 0.8352 (mt) cc_final: 0.8028 (mt) REVERT: E 1063 ASP cc_start: 0.7540 (t0) cc_final: 0.7177 (t0) REVERT: E 1076 ASP cc_start: 0.8337 (t0) cc_final: 0.8034 (t0) REVERT: D 889 LEU cc_start: 0.8292 (mt) cc_final: 0.8002 (mt) REVERT: D 891 TYR cc_start: 0.8098 (m-80) cc_final: 0.7813 (m-80) REVERT: D 1048 SER cc_start: 0.9108 (m) cc_final: 0.8892 (t) REVERT: D 1063 ASP cc_start: 0.7526 (t70) cc_final: 0.7078 (t70) REVERT: D 1077 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7962 (tp40) REVERT: D 1079 CYS cc_start: 0.8358 (t) cc_final: 0.7962 (t) REVERT: C 888 ILE cc_start: 0.7920 (mm) cc_final: 0.7671 (mm) REVERT: C 889 LEU cc_start: 0.8352 (mt) cc_final: 0.8064 (mt) REVERT: C 892 ILE cc_start: 0.8648 (mm) cc_final: 0.8417 (mm) REVERT: C 944 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8322 (mtp-110) REVERT: C 1063 ASP cc_start: 0.7506 (t0) cc_final: 0.7082 (t0) REVERT: B 891 TYR cc_start: 0.8189 (m-80) cc_final: 0.7914 (m-80) REVERT: B 995 SER cc_start: 0.8558 (t) cc_final: 0.8267 (p) outliers start: 77 outliers final: 52 residues processed: 594 average time/residue: 0.3766 time to fit residues: 360.1825 Evaluate side-chains 587 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 535 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 902 PHE Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain F residue 888 ILE Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 970 THR Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 970 THR Chi-restraints excluded: chain E residue 1000 THR Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 888 ILE Chi-restraints excluded: chain D residue 896 VAL Chi-restraints excluded: chain D residue 902 PHE Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 970 THR Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1056 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 125 optimal weight: 2.9990 chunk 469 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 chunk 280 optimal weight: 0.9980 chunk 240 optimal weight: 6.9990 chunk 212 optimal weight: 0.5980 chunk 268 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 333 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN F1096 HIS E1052 HIS E1096 HIS D1096 HIS C1052 HIS C1096 HIS B1096 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.192322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146354 restraints weight = 56911.979| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 4.62 r_work: 0.3520 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29099 Z= 0.157 Angle : 0.458 8.867 40131 Z= 0.256 Chirality : 0.039 0.171 5362 Planarity : 0.003 0.042 5432 Dihedral : 3.808 23.787 5068 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.52 % Allowed : 28.00 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.12), residues: 4865 helix: 3.32 (0.08), residues: 3570 sheet: -0.35 (0.32), residues: 266 loop : -1.74 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.000 TRP D 994 HIS 0.015 0.002 HIS D1096 PHE 0.019 0.001 PHE E 925 TYR 0.009 0.001 TYR C 891 ARG 0.009 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 3005) hydrogen bonds : angle 3.45163 ( 8847) covalent geometry : bond 0.00335 (29099) covalent geometry : angle 0.45815 (40131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 559 time to evaluate : 2.809 Fit side-chains REVERT: A 889 LEU cc_start: 0.8266 (mt) cc_final: 0.7903 (mt) REVERT: A 944 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8222 (mtp-110) REVERT: A 995 SER cc_start: 0.8335 (t) cc_final: 0.8055 (p) REVERT: A 1063 ASP cc_start: 0.7264 (t0) cc_final: 0.6892 (t0) REVERT: G 925 PHE cc_start: 0.7679 (t80) cc_final: 0.7342 (t80) REVERT: G 1063 ASP cc_start: 0.7199 (t70) cc_final: 0.6896 (t0) REVERT: G 1079 CYS cc_start: 0.8020 (t) cc_final: 0.7754 (m) REVERT: F 914 TRP cc_start: 0.6827 (m100) cc_final: 0.6608 (m-10) REVERT: F 1011 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.6844 (m-10) REVERT: F 1053 GLU cc_start: 0.8395 (tt0) cc_final: 0.8105 (tt0) REVERT: F 1063 ASP cc_start: 0.7307 (t70) cc_final: 0.7027 (t0) REVERT: F 1076 ASP cc_start: 0.8519 (t0) cc_final: 0.8297 (t0) REVERT: F 1079 CYS cc_start: 0.8085 (t) cc_final: 0.7779 (m) REVERT: E 889 LEU cc_start: 0.8295 (mt) cc_final: 0.7959 (mt) REVERT: E 1063 ASP cc_start: 0.7349 (t0) cc_final: 0.6936 (t0) REVERT: E 1076 ASP cc_start: 0.8306 (t0) cc_final: 0.8079 (t0) REVERT: D 889 LEU cc_start: 0.8251 (mt) cc_final: 0.7963 (mt) REVERT: D 891 TYR cc_start: 0.8126 (m-80) cc_final: 0.7894 (m-80) REVERT: D 1048 SER cc_start: 0.9111 (m) cc_final: 0.8846 (t) REVERT: D 1063 ASP cc_start: 0.7404 (t70) cc_final: 0.6906 (t70) REVERT: D 1077 GLN cc_start: 0.8384 (tp-100) cc_final: 0.8013 (tp40) REVERT: D 1079 CYS cc_start: 0.8299 (t) cc_final: 0.7909 (t) REVERT: C 889 LEU cc_start: 0.8324 (mt) cc_final: 0.8063 (mt) REVERT: C 890 ASN cc_start: 0.8523 (m-40) cc_final: 0.8316 (m110) REVERT: C 892 ILE cc_start: 0.8645 (mm) cc_final: 0.8410 (mm) REVERT: C 919 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8118 (mt) REVERT: C 944 ARG cc_start: 0.8534 (mtp85) cc_final: 0.8271 (mtp-110) REVERT: C 964 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8420 (mm) REVERT: C 1063 ASP cc_start: 0.7308 (t0) cc_final: 0.6849 (t0) REVERT: C 1088 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: B 891 TYR cc_start: 0.8166 (m-80) cc_final: 0.7902 (m-80) REVERT: B 944 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8286 (mtp180) REVERT: B 995 SER cc_start: 0.8516 (t) cc_final: 0.8214 (p) REVERT: B 1031 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.7135 (mmm160) REVERT: B 1063 ASP cc_start: 0.7318 (t0) cc_final: 0.6546 (t0) outliers start: 68 outliers final: 48 residues processed: 602 average time/residue: 0.3692 time to fit residues: 358.0621 Evaluate side-chains 604 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 552 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 902 PHE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1007 LEU Chi-restraints excluded: chain F residue 1011 TYR Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 VAL Chi-restraints excluded: chain E residue 953 THR Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 902 PHE Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1088 PHE Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 268 optimal weight: 0.4980 chunk 407 optimal weight: 0.0040 chunk 302 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 490 optimal weight: 0.2980 chunk 468 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 421 optimal weight: 0.9990 chunk 472 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 408 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1082 ASN F1082 ASN E1096 HIS C1096 HIS B1082 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.189355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146860 restraints weight = 59287.198| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.61 r_work: 0.3659 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29099 Z= 0.112 Angle : 0.433 7.932 40131 Z= 0.238 Chirality : 0.039 0.178 5362 Planarity : 0.003 0.043 5432 Dihedral : 3.639 23.099 5068 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.36 % Allowed : 29.87 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.12), residues: 4865 helix: 3.53 (0.08), residues: 3556 sheet: 0.01 (0.30), residues: 329 loop : -1.65 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 994 HIS 0.005 0.001 HIS D1096 PHE 0.021 0.001 PHE F 931 TYR 0.015 0.001 TYR C 891 ARG 0.010 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 3005) hydrogen bonds : angle 3.26541 ( 8847) covalent geometry : bond 0.00226 (29099) covalent geometry : angle 0.43348 (40131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 556 time to evaluate : 2.852 Fit side-chains REVERT: A 889 LEU cc_start: 0.8169 (mt) cc_final: 0.7825 (mt) REVERT: A 995 SER cc_start: 0.8170 (t) cc_final: 0.7898 (p) REVERT: A 1063 ASP cc_start: 0.7110 (t0) cc_final: 0.6718 (t0) REVERT: G 925 PHE cc_start: 0.7655 (t80) cc_final: 0.7339 (t80) REVERT: G 995 SER cc_start: 0.8366 (t) cc_final: 0.8094 (p) REVERT: G 1063 ASP cc_start: 0.6987 (t70) cc_final: 0.6688 (t0) REVERT: G 1066 ARG cc_start: 0.7777 (mmp-170) cc_final: 0.7570 (mmp-170) REVERT: G 1079 CYS cc_start: 0.7907 (t) cc_final: 0.7676 (m) REVERT: G 1082 ASN cc_start: 0.8098 (m-40) cc_final: 0.7781 (m110) REVERT: F 889 LEU cc_start: 0.8288 (mt) cc_final: 0.7914 (mt) REVERT: F 914 TRP cc_start: 0.6663 (m100) cc_final: 0.6435 (m-10) REVERT: F 995 SER cc_start: 0.8253 (t) cc_final: 0.7974 (p) REVERT: F 1053 GLU cc_start: 0.8275 (tt0) cc_final: 0.8035 (tt0) REVERT: F 1063 ASP cc_start: 0.7099 (t70) cc_final: 0.6846 (t0) REVERT: F 1076 ASP cc_start: 0.8526 (t0) cc_final: 0.8302 (t0) REVERT: F 1079 CYS cc_start: 0.7973 (t) cc_final: 0.7705 (m) REVERT: E 889 LEU cc_start: 0.8203 (mt) cc_final: 0.7858 (mt) REVERT: E 890 ASN cc_start: 0.8404 (m-40) cc_final: 0.8154 (t0) REVERT: E 995 SER cc_start: 0.8105 (t) cc_final: 0.7850 (p) REVERT: E 1031 ARG cc_start: 0.7386 (mmm160) cc_final: 0.7172 (mmm-85) REVERT: E 1063 ASP cc_start: 0.7168 (t0) cc_final: 0.6896 (t0) REVERT: E 1076 ASP cc_start: 0.8318 (t0) cc_final: 0.8115 (t0) REVERT: E 1093 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8626 (m) REVERT: E 1096 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.5528 (t70) REVERT: D 889 LEU cc_start: 0.8174 (mt) cc_final: 0.7904 (mt) REVERT: D 890 ASN cc_start: 0.8290 (m-40) cc_final: 0.8071 (m-40) REVERT: D 984 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8629 (mtmm) REVERT: D 1063 ASP cc_start: 0.7226 (t70) cc_final: 0.6868 (t70) REVERT: D 1077 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7982 (tp40) REVERT: D 1079 CYS cc_start: 0.8243 (t) cc_final: 0.7849 (t) REVERT: C 889 LEU cc_start: 0.8273 (mt) cc_final: 0.7997 (mt) REVERT: C 890 ASN cc_start: 0.8325 (m-40) cc_final: 0.8114 (m110) REVERT: C 892 ILE cc_start: 0.8521 (mm) cc_final: 0.8295 (mm) REVERT: C 944 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8165 (mtp180) REVERT: C 964 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (mm) REVERT: C 995 SER cc_start: 0.8440 (t) cc_final: 0.8140 (p) REVERT: C 1063 ASP cc_start: 0.7121 (t0) cc_final: 0.6637 (t0) REVERT: C 1088 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: B 891 TYR cc_start: 0.7956 (m-80) cc_final: 0.7689 (m-80) REVERT: B 944 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8280 (mtp-110) REVERT: B 995 SER cc_start: 0.8387 (t) cc_final: 0.8089 (p) REVERT: B 1031 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6984 (mmm160) REVERT: B 1063 ASP cc_start: 0.7093 (t0) cc_final: 0.6321 (t0) outliers start: 66 outliers final: 46 residues processed: 603 average time/residue: 0.3658 time to fit residues: 355.1526 Evaluate side-chains 597 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 547 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1088 PHE Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 902 PHE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 1007 LEU Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1007 LEU Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 VAL Chi-restraints excluded: chain E residue 953 THR Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1093 VAL Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1088 PHE Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 175 optimal weight: 50.0000 chunk 208 optimal weight: 1.9990 chunk 351 optimal weight: 0.9990 chunk 428 optimal weight: 10.0000 chunk 486 optimal weight: 3.9990 chunk 247 optimal weight: 0.0000 chunk 240 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 17 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 252 optimal weight: 50.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN E1096 HIS C1082 ASN C1096 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.190366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144138 restraints weight = 56452.248| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.55 r_work: 0.3504 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 29099 Z= 0.264 Angle : 0.526 8.932 40131 Z= 0.298 Chirality : 0.042 0.198 5362 Planarity : 0.004 0.055 5432 Dihedral : 3.963 24.196 5068 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.41 % Allowed : 30.28 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.12), residues: 4865 helix: 3.30 (0.08), residues: 3549 sheet: -0.17 (0.30), residues: 329 loop : -1.71 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 994 HIS 0.007 0.002 HIS B1096 PHE 0.027 0.002 PHE F1042 TYR 0.012 0.002 TYR D 891 ARG 0.011 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 3005) hydrogen bonds : angle 3.61202 ( 8847) covalent geometry : bond 0.00578 (29099) covalent geometry : angle 0.52649 (40131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 538 time to evaluate : 2.879 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8319 (mt) cc_final: 0.7981 (mt) REVERT: A 995 SER cc_start: 0.8309 (t) cc_final: 0.8018 (p) REVERT: A 1063 ASP cc_start: 0.7380 (t0) cc_final: 0.6935 (t0) REVERT: G 919 LEU cc_start: 0.8485 (mt) cc_final: 0.8284 (mt) REVERT: G 925 PHE cc_start: 0.7674 (t80) cc_final: 0.7347 (t80) REVERT: G 1063 ASP cc_start: 0.7330 (t70) cc_final: 0.7030 (t0) REVERT: G 1079 CYS cc_start: 0.8041 (t) cc_final: 0.7783 (m) REVERT: F 889 LEU cc_start: 0.8289 (mt) cc_final: 0.8011 (mt) REVERT: F 914 TRP cc_start: 0.6868 (m100) cc_final: 0.6655 (m-10) REVERT: F 1011 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: F 1014 ASP cc_start: 0.8517 (t0) cc_final: 0.7689 (m-30) REVERT: F 1016 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7892 (mm-30) REVERT: F 1063 ASP cc_start: 0.7410 (t70) cc_final: 0.7139 (t0) REVERT: F 1076 ASP cc_start: 0.8465 (t0) cc_final: 0.8136 (t0) REVERT: F 1079 CYS cc_start: 0.8031 (t) cc_final: 0.7735 (m) REVERT: E 889 LEU cc_start: 0.8331 (mt) cc_final: 0.8011 (mt) REVERT: E 1063 ASP cc_start: 0.7457 (t0) cc_final: 0.7152 (t0) REVERT: D 889 LEU cc_start: 0.8255 (mt) cc_final: 0.8004 (mt) REVERT: D 984 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8629 (mtmm) REVERT: D 1063 ASP cc_start: 0.7449 (t70) cc_final: 0.7063 (t70) REVERT: D 1077 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8061 (tp40) REVERT: D 1079 CYS cc_start: 0.8270 (t) cc_final: 0.7941 (t) REVERT: C 888 ILE cc_start: 0.7979 (mm) cc_final: 0.7758 (mm) REVERT: C 889 LEU cc_start: 0.8354 (mt) cc_final: 0.8060 (mt) REVERT: C 892 ILE cc_start: 0.8661 (mm) cc_final: 0.8425 (mm) REVERT: C 944 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8104 (mtm180) REVERT: C 964 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (mm) REVERT: C 1063 ASP cc_start: 0.7356 (t0) cc_final: 0.6843 (t0) REVERT: B 891 TYR cc_start: 0.8228 (m-80) cc_final: 0.7970 (m-80) REVERT: B 944 ARG cc_start: 0.8645 (mtp85) cc_final: 0.8363 (mtp-110) REVERT: B 995 SER cc_start: 0.8490 (t) cc_final: 0.8177 (p) REVERT: B 1014 ASP cc_start: 0.8513 (t0) cc_final: 0.7815 (m-30) REVERT: B 1031 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7107 (mmm160) REVERT: B 1063 ASP cc_start: 0.7379 (t0) cc_final: 0.6608 (t0) outliers start: 79 outliers final: 60 residues processed: 592 average time/residue: 0.3914 time to fit residues: 370.2154 Evaluate side-chains 597 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 535 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 902 PHE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1011 TYR Chi-restraints excluded: chain F residue 1021 VAL Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 VAL Chi-restraints excluded: chain E residue 970 THR Chi-restraints excluded: chain E residue 1009 VAL Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 902 PHE Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 256 optimal weight: 0.9980 chunk 465 optimal weight: 50.0000 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 424 optimal weight: 2.9990 chunk 246 optimal weight: 50.0000 chunk 242 optimal weight: 20.0000 chunk 457 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN E1096 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.187896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150085 restraints weight = 62453.816| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 4.79 r_work: 0.3530 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 29099 Z= 0.298 Angle : 0.555 9.606 40131 Z= 0.316 Chirality : 0.042 0.194 5362 Planarity : 0.004 0.054 5432 Dihedral : 4.164 24.871 5068 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.90 % Allowed : 29.79 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.12), residues: 4865 helix: 2.98 (0.08), residues: 3570 sheet: -0.23 (0.30), residues: 329 loop : -1.92 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 994 HIS 0.009 0.003 HIS D1094 PHE 0.033 0.002 PHE F1042 TYR 0.015 0.002 TYR D 891 ARG 0.012 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 3005) hydrogen bonds : angle 3.81653 ( 8847) covalent geometry : bond 0.00653 (29099) covalent geometry : angle 0.55532 (40131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 552 time to evaluate : 4.423 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8347 (mt) cc_final: 0.8008 (mt) REVERT: A 944 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8275 (mtp180) REVERT: A 995 SER cc_start: 0.8362 (t) cc_final: 0.8062 (p) REVERT: A 1014 ASP cc_start: 0.8537 (t0) cc_final: 0.7668 (m-30) REVERT: A 1063 ASP cc_start: 0.7425 (t0) cc_final: 0.6983 (t0) REVERT: A 1066 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7658 (mmp80) REVERT: G 925 PHE cc_start: 0.7773 (t80) cc_final: 0.7419 (t80) REVERT: G 1063 ASP cc_start: 0.7390 (t70) cc_final: 0.7096 (t0) REVERT: G 1079 CYS cc_start: 0.7987 (t) cc_final: 0.7691 (m) REVERT: F 889 LEU cc_start: 0.8359 (mt) cc_final: 0.8091 (mt) REVERT: F 1011 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.6958 (m-10) REVERT: F 1014 ASP cc_start: 0.8493 (t0) cc_final: 0.7804 (m-30) REVERT: F 1016 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7937 (mm-30) REVERT: F 1053 GLU cc_start: 0.8391 (tt0) cc_final: 0.8128 (tt0) REVERT: F 1063 ASP cc_start: 0.7464 (t70) cc_final: 0.7204 (t0) REVERT: F 1066 ARG cc_start: 0.7934 (mmm160) cc_final: 0.7666 (mmp80) REVERT: F 1076 ASP cc_start: 0.8425 (t0) cc_final: 0.8077 (t0) REVERT: F 1079 CYS cc_start: 0.8042 (t) cc_final: 0.7801 (m) REVERT: E 889 LEU cc_start: 0.8361 (mt) cc_final: 0.8047 (mt) REVERT: E 1063 ASP cc_start: 0.7663 (t0) cc_final: 0.7250 (t0) REVERT: D 889 LEU cc_start: 0.8245 (mt) cc_final: 0.7992 (mt) REVERT: D 984 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8576 (mtmm) REVERT: D 1063 ASP cc_start: 0.7509 (t70) cc_final: 0.7100 (t70) REVERT: D 1077 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8015 (tp40) REVERT: C 888 ILE cc_start: 0.8031 (mm) cc_final: 0.7826 (mm) REVERT: C 889 LEU cc_start: 0.8351 (mt) cc_final: 0.8029 (mt) REVERT: C 892 ILE cc_start: 0.8640 (mm) cc_final: 0.8415 (mm) REVERT: C 944 ARG cc_start: 0.8339 (mtp85) cc_final: 0.7929 (mtm180) REVERT: C 1011 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: C 1063 ASP cc_start: 0.7397 (t0) cc_final: 0.6886 (t0) REVERT: B 891 TYR cc_start: 0.8136 (m-80) cc_final: 0.7876 (m-80) REVERT: B 944 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8250 (mtp-110) REVERT: B 995 SER cc_start: 0.8497 (t) cc_final: 0.8169 (p) REVERT: B 1031 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6999 (mmm160) REVERT: B 1063 ASP cc_start: 0.7433 (t0) cc_final: 0.6632 (t0) REVERT: B 1083 ASP cc_start: 0.8476 (t0) cc_final: 0.8264 (t0) outliers start: 85 outliers final: 73 residues processed: 611 average time/residue: 0.4985 time to fit residues: 492.5106 Evaluate side-chains 623 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 548 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 902 PHE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain G residue 1000 THR Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 970 THR Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1007 LEU Chi-restraints excluded: chain F residue 1011 TYR Chi-restraints excluded: chain F residue 1021 VAL Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 946 VAL Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 970 THR Chi-restraints excluded: chain E residue 1000 THR Chi-restraints excluded: chain E residue 1009 VAL Chi-restraints excluded: chain E residue 1020 LYS Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 902 PHE Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1034 HIS Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1011 TYR Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 49 optimal weight: 4.9990 chunk 128 optimal weight: 0.0370 chunk 50 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 430 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 343 optimal weight: 0.7980 chunk 376 optimal weight: 20.0000 chunk 324 optimal weight: 30.0000 chunk 140 optimal weight: 2.9990 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1082 ASN F1082 ASN E1096 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.188433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150386 restraints weight = 62874.889| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 4.30 r_work: 0.3569 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29099 Z= 0.251 Angle : 0.532 9.277 40131 Z= 0.299 Chirality : 0.042 0.201 5362 Planarity : 0.004 0.047 5432 Dihedral : 4.122 24.801 5068 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.74 % Allowed : 30.19 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.12), residues: 4865 helix: 2.98 (0.08), residues: 3570 sheet: 0.05 (0.35), residues: 259 loop : -1.95 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 994 HIS 0.007 0.002 HIS B1096 PHE 0.028 0.002 PHE F1042 TYR 0.010 0.001 TYR D 891 ARG 0.013 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 3005) hydrogen bonds : angle 3.74929 ( 8847) covalent geometry : bond 0.00548 (29099) covalent geometry : angle 0.53177 (40131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 546 time to evaluate : 4.694 Fit side-chains REVERT: A 889 LEU cc_start: 0.8300 (mt) cc_final: 0.7953 (mt) REVERT: A 944 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8270 (mtp-110) REVERT: A 995 SER cc_start: 0.8263 (t) cc_final: 0.7959 (p) REVERT: A 1063 ASP cc_start: 0.7361 (t0) cc_final: 0.6919 (t0) REVERT: G 925 PHE cc_start: 0.7796 (t80) cc_final: 0.7429 (t80) REVERT: G 1063 ASP cc_start: 0.7314 (t70) cc_final: 0.7015 (t0) REVERT: G 1079 CYS cc_start: 0.7975 (t) cc_final: 0.7658 (m) REVERT: F 889 LEU cc_start: 0.8348 (mt) cc_final: 0.8081 (mt) REVERT: F 1011 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: F 1014 ASP cc_start: 0.8448 (t0) cc_final: 0.7794 (m-30) REVERT: F 1016 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7942 (mm-30) REVERT: F 1053 GLU cc_start: 0.8372 (tt0) cc_final: 0.8106 (tt0) REVERT: F 1063 ASP cc_start: 0.7409 (t70) cc_final: 0.7148 (t0) REVERT: F 1066 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7598 (mmp80) REVERT: F 1076 ASP cc_start: 0.8399 (t0) cc_final: 0.8046 (t0) REVERT: F 1079 CYS cc_start: 0.8022 (t) cc_final: 0.7761 (m) REVERT: E 889 LEU cc_start: 0.8362 (mt) cc_final: 0.8053 (mt) REVERT: E 1063 ASP cc_start: 0.7634 (t0) cc_final: 0.7223 (t0) REVERT: D 889 LEU cc_start: 0.8227 (mt) cc_final: 0.7969 (mt) REVERT: D 984 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8652 (mtmm) REVERT: D 1014 ASP cc_start: 0.8357 (t0) cc_final: 0.7629 (m-30) REVERT: D 1063 ASP cc_start: 0.7412 (t70) cc_final: 0.7031 (t70) REVERT: D 1077 GLN cc_start: 0.8345 (tp-100) cc_final: 0.8029 (tp40) REVERT: D 1079 CYS cc_start: 0.8291 (t) cc_final: 0.7843 (t) REVERT: C 888 ILE cc_start: 0.7999 (mm) cc_final: 0.7763 (mm) REVERT: C 889 LEU cc_start: 0.8337 (mt) cc_final: 0.8023 (mt) REVERT: C 892 ILE cc_start: 0.8535 (mm) cc_final: 0.8312 (mm) REVERT: C 944 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7888 (mtm180) REVERT: C 1063 ASP cc_start: 0.7313 (t0) cc_final: 0.6796 (t0) REVERT: B 891 TYR cc_start: 0.7987 (m-80) cc_final: 0.7669 (m-80) REVERT: B 944 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8283 (mtp-110) REVERT: B 995 SER cc_start: 0.8472 (t) cc_final: 0.8131 (p) REVERT: B 1014 ASP cc_start: 0.8473 (t0) cc_final: 0.7768 (m-30) REVERT: B 1031 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.6993 (mmm160) REVERT: B 1063 ASP cc_start: 0.7362 (t0) cc_final: 0.6443 (t0) REVERT: B 1083 ASP cc_start: 0.8463 (t0) cc_final: 0.8232 (t0) outliers start: 83 outliers final: 69 residues processed: 601 average time/residue: 0.4688 time to fit residues: 450.6428 Evaluate side-chains 610 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 540 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain G residue 1000 THR Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 853 SER Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1007 LEU Chi-restraints excluded: chain F residue 1011 TYR Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 970 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1009 VAL Chi-restraints excluded: chain E residue 1020 LYS Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1034 HIS Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 902 PHE Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 243 optimal weight: 0.3980 chunk 166 optimal weight: 30.0000 chunk 345 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 362 optimal weight: 8.9990 chunk 193 optimal weight: 0.6980 chunk 469 optimal weight: 3.9990 chunk 324 optimal weight: 9.9990 chunk 314 optimal weight: 4.9990 chunk 471 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN ** E1096 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1082 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.189397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.151723 restraints weight = 62758.106| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 4.55 r_work: 0.3558 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29099 Z= 0.196 Angle : 0.501 8.694 40131 Z= 0.279 Chirality : 0.040 0.204 5362 Planarity : 0.004 0.051 5432 Dihedral : 3.991 24.526 5068 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.41 % Allowed : 30.68 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.12), residues: 4865 helix: 3.14 (0.08), residues: 3570 sheet: 0.13 (0.35), residues: 259 loop : -1.90 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 994 HIS 0.007 0.002 HIS F1096 PHE 0.025 0.002 PHE E 925 TYR 0.008 0.001 TYR D 891 ARG 0.014 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 3005) hydrogen bonds : angle 3.60321 ( 8847) covalent geometry : bond 0.00425 (29099) covalent geometry : angle 0.50078 (40131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 540 time to evaluate : 2.865 Fit side-chains REVERT: A 889 LEU cc_start: 0.8287 (mt) cc_final: 0.7940 (mt) REVERT: A 995 SER cc_start: 0.8307 (t) cc_final: 0.7997 (p) REVERT: A 1014 ASP cc_start: 0.8516 (t0) cc_final: 0.7611 (m-30) REVERT: A 1063 ASP cc_start: 0.7319 (t0) cc_final: 0.6853 (t0) REVERT: G 925 PHE cc_start: 0.7761 (t80) cc_final: 0.7397 (t80) REVERT: G 1063 ASP cc_start: 0.7204 (t70) cc_final: 0.6872 (t0) REVERT: G 1079 CYS cc_start: 0.7974 (t) cc_final: 0.7657 (m) REVERT: F 889 LEU cc_start: 0.8344 (mt) cc_final: 0.8068 (mt) REVERT: F 1014 ASP cc_start: 0.8383 (t0) cc_final: 0.7713 (m-30) REVERT: F 1016 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7899 (mm-30) REVERT: F 1053 GLU cc_start: 0.8404 (tt0) cc_final: 0.8123 (tt0) REVERT: F 1063 ASP cc_start: 0.7353 (t70) cc_final: 0.7059 (t0) REVERT: F 1076 ASP cc_start: 0.8423 (t0) cc_final: 0.8055 (t0) REVERT: F 1079 CYS cc_start: 0.8080 (t) cc_final: 0.7789 (m) REVERT: E 889 LEU cc_start: 0.8346 (mt) cc_final: 0.8031 (mt) REVERT: E 1063 ASP cc_start: 0.7559 (t0) cc_final: 0.7139 (t0) REVERT: D 889 LEU cc_start: 0.8213 (mt) cc_final: 0.7951 (mt) REVERT: D 984 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8557 (mtmm) REVERT: D 1063 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6987 (t70) REVERT: D 1077 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8035 (tp40) REVERT: D 1079 CYS cc_start: 0.8299 (t) cc_final: 0.7837 (t) REVERT: C 888 ILE cc_start: 0.7994 (mm) cc_final: 0.7764 (mm) REVERT: C 889 LEU cc_start: 0.8330 (mt) cc_final: 0.8020 (mt) REVERT: C 890 ASN cc_start: 0.8456 (m-40) cc_final: 0.8208 (m-40) REVERT: C 892 ILE cc_start: 0.8513 (mm) cc_final: 0.8291 (mm) REVERT: C 944 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7897 (mtm180) REVERT: C 1063 ASP cc_start: 0.7231 (t0) cc_final: 0.6713 (t0) REVERT: B 891 TYR cc_start: 0.7941 (m-80) cc_final: 0.7629 (m-80) REVERT: B 944 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8232 (mtp-110) REVERT: B 995 SER cc_start: 0.8497 (t) cc_final: 0.8162 (p) REVERT: B 1014 ASP cc_start: 0.8463 (t0) cc_final: 0.7758 (m-30) REVERT: B 1031 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.6961 (mmm160) REVERT: B 1063 ASP cc_start: 0.7303 (t0) cc_final: 0.6342 (t0) REVERT: B 1083 ASP cc_start: 0.8447 (t0) cc_final: 0.8202 (t0) outliers start: 79 outliers final: 70 residues processed: 593 average time/residue: 0.4081 time to fit residues: 389.3858 Evaluate side-chains 607 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 536 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 PHE Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain G residue 970 THR Chi-restraints excluded: chain G residue 1000 THR Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 853 SER Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 953 THR Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1007 LEU Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 970 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1009 VAL Chi-restraints excluded: chain E residue 1020 LYS Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1034 HIS Chi-restraints excluded: chain D residue 1063 ASP Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 390 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 311 optimal weight: 20.0000 chunk 408 optimal weight: 0.9980 chunk 388 optimal weight: 50.0000 chunk 6 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 444 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN E1096 HIS C1082 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.189677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153119 restraints weight = 62732.828| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 4.98 r_work: 0.3587 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29099 Z= 0.190 Angle : 0.501 8.485 40131 Z= 0.277 Chirality : 0.040 0.222 5362 Planarity : 0.004 0.053 5432 Dihedral : 3.933 24.411 5068 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.01 % Allowed : 31.09 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.12), residues: 4865 helix: 3.24 (0.08), residues: 3570 sheet: 0.15 (0.35), residues: 259 loop : -1.87 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 994 HIS 0.006 0.002 HIS E1096 PHE 0.023 0.002 PHE C 934 TYR 0.008 0.001 TYR D 891 ARG 0.014 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 3005) hydrogen bonds : angle 3.54061 ( 8847) covalent geometry : bond 0.00414 (29099) covalent geometry : angle 0.50076 (40131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9730 Ramachandran restraints generated. 4865 Oldfield, 0 Emsley, 4865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 534 time to evaluate : 3.024 Fit side-chains REVERT: A 889 LEU cc_start: 0.8285 (mt) cc_final: 0.7946 (mt) REVERT: A 995 SER cc_start: 0.8283 (t) cc_final: 0.7990 (p) REVERT: A 1014 ASP cc_start: 0.8450 (t0) cc_final: 0.7662 (m-30) REVERT: A 1063 ASP cc_start: 0.7366 (t0) cc_final: 0.6891 (t0) REVERT: G 925 PHE cc_start: 0.7854 (t80) cc_final: 0.7499 (t80) REVERT: G 1063 ASP cc_start: 0.7210 (t70) cc_final: 0.6888 (t0) REVERT: G 1079 CYS cc_start: 0.7999 (t) cc_final: 0.7668 (m) REVERT: F 889 LEU cc_start: 0.8338 (mt) cc_final: 0.8067 (mt) REVERT: F 1014 ASP cc_start: 0.8414 (t0) cc_final: 0.7716 (m-30) REVERT: F 1016 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7961 (mm-30) REVERT: F 1063 ASP cc_start: 0.7339 (t70) cc_final: 0.7013 (t0) REVERT: F 1066 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7586 (mmp80) REVERT: F 1076 ASP cc_start: 0.8449 (t0) cc_final: 0.8223 (t0) REVERT: E 889 LEU cc_start: 0.8365 (mt) cc_final: 0.8050 (mt) REVERT: E 1063 ASP cc_start: 0.7564 (t0) cc_final: 0.7166 (t0) REVERT: E 1088 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: D 889 LEU cc_start: 0.8204 (mt) cc_final: 0.7944 (mt) REVERT: D 984 LYS cc_start: 0.8927 (mtmt) cc_final: 0.8639 (mtmm) REVERT: D 1063 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7023 (t70) REVERT: D 1077 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8050 (tp40) REVERT: D 1079 CYS cc_start: 0.8328 (t) cc_final: 0.7867 (t) REVERT: C 889 LEU cc_start: 0.8339 (mt) cc_final: 0.8066 (mt) REVERT: C 890 ASN cc_start: 0.8516 (m-40) cc_final: 0.8270 (m-40) REVERT: C 892 ILE cc_start: 0.8555 (mm) cc_final: 0.8328 (mm) REVERT: C 944 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7983 (mtm180) REVERT: C 1063 ASP cc_start: 0.7217 (t0) cc_final: 0.6676 (t0) REVERT: B 891 TYR cc_start: 0.7981 (m-80) cc_final: 0.7687 (m-80) REVERT: B 944 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8262 (mtp-110) REVERT: B 995 SER cc_start: 0.8476 (t) cc_final: 0.8147 (p) REVERT: B 1014 ASP cc_start: 0.8446 (t0) cc_final: 0.7770 (m-30) REVERT: B 1031 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.6943 (mmm160) REVERT: B 1063 ASP cc_start: 0.7293 (t0) cc_final: 0.6327 (t0) REVERT: B 1083 ASP cc_start: 0.8497 (t0) cc_final: 0.8231 (t0) outliers start: 74 outliers final: 69 residues processed: 585 average time/residue: 0.4099 time to fit residues: 387.2389 Evaluate side-chains 605 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 534 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 927 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 894 ILE Chi-restraints excluded: chain G residue 902 PHE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain G residue 970 THR Chi-restraints excluded: chain G residue 1000 THR Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 1004 VAL Chi-restraints excluded: chain F residue 1007 LEU Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1089 ASN Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 902 PHE Chi-restraints excluded: chain E residue 927 LEU Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 960 THR Chi-restraints excluded: chain E residue 970 THR Chi-restraints excluded: chain E residue 1000 THR Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1009 VAL Chi-restraints excluded: chain E residue 1020 LYS Chi-restraints excluded: chain E residue 1088 PHE Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 927 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 960 THR Chi-restraints excluded: chain D residue 970 THR Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1034 HIS Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1063 ASP Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 927 LEU Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 953 THR Chi-restraints excluded: chain C residue 960 THR Chi-restraints excluded: chain C residue 1000 THR Chi-restraints excluded: chain C residue 1007 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1096 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 264 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 347 optimal weight: 0.9980 chunk 465 optimal weight: 20.0000 chunk 303 optimal weight: 0.4980 chunk 448 optimal weight: 7.9990 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN E1096 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.185575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148394 restraints weight = 62865.225| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 4.41 r_work: 0.3537 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.009 0.095 29099 Z= 0.415 Angle : 0.660 10.968 40131 Z= 0.379 Chirality : 0.046 0.237 5362 Planarity : 0.005 0.060 5432 Dihedral : 4.601 25.433 5068 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.01 % Allowed : 31.57 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.12), residues: 4865 helix: 2.51 (0.09), residues: 3507 sheet: -0.42 (0.29), residues: 329 loop : -2.11 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 994 HIS 0.015 0.003 HIS E1096 PHE 0.051 0.003 PHE F1042 TYR 0.018 0.003 TYR C 891 ARG 0.015 0.001 ARG G1031 Details of bonding type rmsd hydrogen bonds : bond 0.05446 ( 3005) hydrogen bonds : angle 4.27733 ( 8847) covalent geometry : bond 0.00915 (29099) covalent geometry : angle 0.65982 (40131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19710.07 seconds wall clock time: 341 minutes 29.69 seconds (20489.69 seconds total)