Starting phenix.real_space_refine on Fri Mar 6 06:43:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ux1_26845/03_2026/7ux1_26845.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ux1_26845/03_2026/7ux1_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ux1_26845/03_2026/7ux1_26845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ux1_26845/03_2026/7ux1_26845.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ux1_26845/03_2026/7ux1_26845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ux1_26845/03_2026/7ux1_26845.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} 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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} 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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} 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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} 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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} 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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} 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, 'GLU:plan': 28, 'ASN:plan1': 25, 'ARG:plan': 27, 'TRP:plan': 18, 'TYR:plan': 7, 'ASP:plan': 16, 'PHE:plan': 20, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 892 Time building chain proxies: 6.14, per 1000 atoms: 0.21 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 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: 0.98 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: 6.07 Time building geometry restraints manager: 3.44 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'F' selection = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' } 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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.540 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- 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 : 6.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.005 0.001 ARG C 944 TYR 0.006 0.001 TYR F1011 PHE 0.006 0.001 PHE D1042 TRP 0.006 0.001 TRP B 857 HIS 0.002 0.001 HIS C1052 Details of bonding type rmsd covalent geometry : bond 0.00275 (29099) covalent geometry : angle 0.55975 (40131) hydrogen bonds : bond 0.11407 ( 3005) hydrogen bonds : angle 3.99676 ( 8847) *********************** 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 : 0.961 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: 0.1716 time to fit residues: 154.1898 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 : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 0.7980 chunk 261 optimal weight: 0.0270 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.1980 overall best weight: 0.7240 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.193979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151048 restraints weight = 56830.703| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.88 r_work: 0.3558 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29099 Z= 0.127 Angle : 0.444 8.764 40131 Z= 0.245 Chirality : 0.039 0.156 5362 Planarity : 0.003 0.043 5432 Dihedral : 3.636 22.335 5068 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.14 % Allowed : 29.06 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.13), residues: 4865 helix: 3.38 (0.08), residues: 3584 sheet: -0.13 (0.29), residues: 343 loop : -1.79 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E1031 TYR 0.007 0.001 TYR B 891 PHE 0.013 0.001 PHE D1045 TRP 0.006 0.001 TRP D 857 HIS 0.005 0.001 HIS B1096 Details of bonding type rmsd covalent geometry : bond 0.00256 (29099) covalent geometry : angle 0.44446 (40131) hydrogen bonds : bond 0.03657 ( 3005) hydrogen bonds : angle 3.37918 ( 8847) *********************** 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 600 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 549 time to evaluate : 1.012 Fit side-chains REVERT: A 889 LEU cc_start: 0.8289 (mt) cc_final: 0.7968 (mt) REVERT: A 944 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8264 (mtp-110) REVERT: A 995 SER cc_start: 0.8408 (t) cc_final: 0.8108 (p) REVERT: A 1063 ASP cc_start: 0.7143 (t0) cc_final: 0.6863 (t0) REVERT: A 1079 CYS cc_start: 0.8404 (t) cc_final: 0.7995 (m) REVERT: G 889 LEU cc_start: 0.8152 (mt) cc_final: 0.7666 (mt) REVERT: F 1031 ARG cc_start: 0.7565 (mmm160) cc_final: 0.6757 (mmm160) REVERT: F 1063 ASP cc_start: 0.7278 (t70) cc_final: 0.6303 (t0) REVERT: F 1066 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7526 (mmp80) REVERT: F 1076 ASP cc_start: 0.8606 (t0) cc_final: 0.8258 (t0) REVERT: F 1079 CYS cc_start: 0.8105 (t) cc_final: 0.7791 (m) REVERT: F 1093 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8522 (m) REVERT: E 889 LEU cc_start: 0.8173 (mt) cc_final: 0.7837 (mt) REVERT: E 890 ASN cc_start: 0.8664 (m-40) cc_final: 0.8454 (t0) REVERT: E 995 SER cc_start: 0.8228 (t) cc_final: 0.7961 (p) REVERT: E 1031 ARG cc_start: 0.7452 (mmm160) cc_final: 0.7207 (mmm-85) REVERT: E 1063 ASP cc_start: 0.7258 (t0) cc_final: 0.7012 (t0) REVERT: E 1076 ASP cc_start: 0.8386 (t0) cc_final: 0.8083 (t0) REVERT: D 889 LEU cc_start: 0.8221 (mt) cc_final: 0.7881 (mt) REVERT: D 893 ILE cc_start: 0.8613 (mm) cc_final: 0.8412 (mm) REVERT: D 1063 ASP cc_start: 0.7339 (t70) cc_final: 0.7098 (t70) REVERT: C 889 LEU cc_start: 0.8241 (mt) cc_final: 0.7972 (mt) REVERT: C 892 ILE cc_start: 0.8610 (mm) cc_final: 0.8381 (mm) REVERT: C 970 THR cc_start: 0.8820 (p) cc_final: 0.8586 (m) REVERT: C 1053 GLU cc_start: 0.8378 (tt0) cc_final: 0.8063 (tt0) REVERT: C 1063 ASP cc_start: 0.7280 (t0) cc_final: 0.6975 (t0) REVERT: C 1079 CYS cc_start: 0.8273 (t) cc_final: 0.7965 (m) REVERT: B 891 TYR cc_start: 0.8077 (m-80) cc_final: 0.7766 (m-80) REVERT: B 927 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7050 (mp) REVERT: B 984 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8456 (mtmm) REVERT: B 995 SER cc_start: 0.8581 (t) cc_final: 0.8315 (p) REVERT: B 1063 ASP cc_start: 0.7159 (t0) cc_final: 0.6781 (t0) outliers start: 51 outliers final: 35 residues processed: 580 average time/residue: 0.1702 time to fit residues: 158.3739 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 : 0.980 ------------------------------------------------------------------------------- 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 892 ILE 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 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 354 optimal weight: 0.7980 chunk 353 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 433 optimal weight: 0.0870 chunk 301 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 166 optimal weight: 40.0000 chunk 227 optimal weight: 0.9990 chunk 435 optimal weight: 20.0000 chunk 233 optimal weight: 30.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1082 ASN G1096 HIS F1096 HIS E1096 HIS D1096 HIS C1096 HIS B1082 ASN B1096 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.194112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143989 restraints weight = 56764.765| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 4.22 r_work: 0.3589 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1097 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= 0.125 Angle : 0.436 8.187 40131 Z= 0.240 Chirality : 0.039 0.156 5362 Planarity : 0.003 0.039 5432 Dihedral : 3.602 22.624 5068 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.36 % Allowed : 28.33 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.12), residues: 4865 helix: 3.52 (0.08), residues: 3556 sheet: -0.00 (0.30), residues: 329 loop : -1.80 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G1031 TYR 0.008 0.001 TYR E 891 PHE 0.011 0.001 PHE C1045 TRP 0.004 0.000 TRP A 994 HIS 0.007 0.001 HIS G1094 Details of bonding type rmsd covalent geometry : bond 0.00256 (29099) covalent geometry : angle 0.43556 (40131) hydrogen bonds : bond 0.03601 ( 3005) hydrogen bonds : angle 3.28342 ( 8847) *********************** 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 618 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 552 time to evaluate : 0.907 Fit side-chains REVERT: A 889 LEU cc_start: 0.8262 (mt) cc_final: 0.7932 (mt) REVERT: A 944 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8187 (mtp-110) REVERT: A 970 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8466 (m) REVERT: A 995 SER cc_start: 0.8233 (t) cc_final: 0.7955 (p) REVERT: A 1063 ASP cc_start: 0.7060 (t0) cc_final: 0.6749 (t0) REVERT: A 1079 CYS cc_start: 0.8365 (t) cc_final: 0.8013 (m) REVERT: G 925 PHE cc_start: 0.7593 (t80) cc_final: 0.7325 (t80) REVERT: G 995 SER cc_start: 0.8330 (t) cc_final: 0.8042 (p) REVERT: G 1063 ASP cc_start: 0.6978 (t0) cc_final: 0.6682 (t0) REVERT: G 1079 CYS cc_start: 0.7941 (t) cc_final: 0.7673 (m) REVERT: F 995 SER cc_start: 0.8301 (t) cc_final: 0.8050 (p) REVERT: F 1063 ASP cc_start: 0.7153 (t70) cc_final: 0.6836 (t0) REVERT: F 1066 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7520 (mmp80) REVERT: F 1076 ASP cc_start: 0.8587 (t0) cc_final: 0.8347 (t0) REVERT: F 1079 CYS cc_start: 0.8035 (t) cc_final: 0.7790 (m) REVERT: F 1093 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8653 (m) REVERT: E 889 LEU cc_start: 0.8178 (mt) cc_final: 0.7851 (mt) REVERT: E 890 ASN cc_start: 0.8626 (m-40) cc_final: 0.8391 (t0) REVERT: E 995 SER cc_start: 0.8124 (t) cc_final: 0.7870 (p) REVERT: E 1063 ASP cc_start: 0.7185 (t0) cc_final: 0.6858 (t0) REVERT: E 1076 ASP cc_start: 0.8405 (t0) cc_final: 0.8096 (t0) REVERT: E 1083 ASP cc_start: 0.8762 (t0) cc_final: 0.8510 (t0) REVERT: D 889 LEU cc_start: 0.8214 (mt) cc_final: 0.7887 (mt) REVERT: D 890 ASN cc_start: 0.8373 (m-40) cc_final: 0.8107 (m-40) REVERT: D 891 TYR cc_start: 0.8053 (m-80) cc_final: 0.7583 (m-80) REVERT: D 893 ILE cc_start: 0.8544 (mm) cc_final: 0.8343 (mm) REVERT: D 1063 ASP cc_start: 0.7218 (t70) cc_final: 0.6975 (t70) REVERT: C 889 LEU cc_start: 0.8266 (mt) cc_final: 0.7988 (mt) REVERT: C 890 ASN cc_start: 0.8516 (m-40) cc_final: 0.8174 (m110) REVERT: C 892 ILE cc_start: 0.8605 (mm) cc_final: 0.8365 (mm) REVERT: C 970 THR cc_start: 0.8768 (p) cc_final: 0.8538 (m) REVERT: C 995 SER cc_start: 0.8481 (t) cc_final: 0.8194 (p) REVERT: C 1063 ASP cc_start: 0.7197 (t0) cc_final: 0.6826 (t0) REVERT: B 891 TYR cc_start: 0.8089 (m-80) cc_final: 0.7780 (m-80) REVERT: B 927 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 944 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8283 (mtp-110) REVERT: B 984 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8517 (mtmm) REVERT: B 995 SER cc_start: 0.8510 (t) cc_final: 0.8242 (p) REVERT: B 1063 ASP cc_start: 0.6963 (t0) cc_final: 0.6652 (t0) outliers start: 66 outliers final: 48 residues processed: 590 average time/residue: 0.1679 time to fit residues: 159.0841 Evaluate side-chains 593 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 542 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 970 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1056 LEU 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 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain F residue 902 PHE Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 953 THR Chi-restraints excluded: chain F residue 960 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 1093 VAL 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 1000 THR Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain E residue 1091 LEU 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 1056 LEU Chi-restraints excluded: chain C residue 870 LEU 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 942 PHE 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 1056 LEU Chi-restraints excluded: chain B residue 888 ILE 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 953 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 LEU 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 253 optimal weight: 40.0000 chunk 58 optimal weight: 0.7980 chunk 110 optimal weight: 50.0000 chunk 432 optimal weight: 7.9990 chunk 467 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 382 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 464 optimal weight: 20.0000 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 933 ASN F1052 HIS ** F1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1052 HIS C1052 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.189029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141742 restraints weight = 54825.493| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 5.02 r_work: 0.3368 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.147 29099 Z= 0.726 Angle : 0.920 14.815 40131 Z= 0.537 Chirality : 0.058 0.274 5362 Planarity : 0.007 0.095 5432 Dihedral : 5.572 26.919 5068 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 9.33 % Allowed : 26.30 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.12), residues: 4865 helix: 1.18 (0.09), residues: 3549 sheet: -0.70 (0.29), residues: 315 loop : -2.03 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG E1073 TYR 0.028 0.005 TYR C1011 PHE 0.075 0.005 PHE F1042 TRP 0.023 0.002 TRP D 994 HIS 0.025 0.006 HIS C1096 Details of bonding type rmsd covalent geometry : bond 0.01606 (29099) covalent geometry : angle 0.91964 (40131) hydrogen bonds : bond 0.07388 ( 3005) hydrogen bonds : angle 5.41349 ( 8847) *********************** 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 668 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 553 time to evaluate : 0.955 Fit side-chains REVERT: A 889 LEU cc_start: 0.8497 (mt) cc_final: 0.8254 (mt) REVERT: A 925 PHE cc_start: 0.7552 (t80) cc_final: 0.7300 (t80) REVERT: A 942 PHE cc_start: 0.7613 (m-10) cc_final: 0.7388 (m-80) REVERT: A 1063 ASP cc_start: 0.7789 (t0) cc_final: 0.7382 (t0) REVERT: A 1076 ASP cc_start: 0.8445 (t0) cc_final: 0.8167 (t0) REVERT: G 888 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7960 (mt) REVERT: G 893 ILE cc_start: 0.8793 (mm) cc_final: 0.8573 (mm) REVERT: G 1063 ASP cc_start: 0.7622 (t0) cc_final: 0.7333 (t0) REVERT: G 1066 ARG cc_start: 0.8086 (mmp-170) cc_final: 0.7807 (mmp-170) REVERT: F 889 LEU cc_start: 0.8539 (mt) cc_final: 0.8218 (mt) REVERT: F 964 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8546 (mm) REVERT: F 1011 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: F 1063 ASP cc_start: 0.7661 (t70) cc_final: 0.7428 (t0) REVERT: F 1076 ASP cc_start: 0.8460 (t0) cc_final: 0.8258 (t0) REVERT: E 1063 ASP cc_start: 0.7825 (t0) cc_final: 0.7435 (t0) REVERT: D 889 LEU cc_start: 0.8444 (mt) cc_final: 0.8193 (mt) REVERT: D 1063 ASP cc_start: 0.7824 (t70) cc_final: 0.7333 (t70) REVERT: D 1077 GLN cc_start: 0.8343 (tp-100) cc_final: 0.8092 (tp40) REVERT: C 888 ILE cc_start: 0.8148 (mm) cc_final: 0.7914 (mm) REVERT: C 889 LEU cc_start: 0.8479 (mt) cc_final: 0.8176 (mt) REVERT: C 892 ILE cc_start: 0.8733 (mm) cc_final: 0.8498 (mm) REVERT: C 1063 ASP cc_start: 0.7757 (t0) cc_final: 0.7233 (t0) REVERT: C 1088 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: B 891 TYR cc_start: 0.8300 (m-80) cc_final: 0.7998 (m-80) REVERT: B 930 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7236 (tt) REVERT: B 944 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8380 (mtp180) REVERT: B 1031 ARG cc_start: 0.7698 (mmm160) cc_final: 0.6905 (mmm160) REVERT: B 1063 ASP cc_start: 0.7603 (t0) cc_final: 0.7180 (t0) outliers start: 115 outliers final: 85 residues processed: 633 average time/residue: 0.1625 time to fit residues: 166.1508 Evaluate side-chains 638 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 548 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 902 PHE Chi-restraints excluded: chain A residue 912 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 1023 LEU Chi-restraints excluded: chain A residue 1034 HIS Chi-restraints excluded: chain A residue 1042 PHE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1091 LEU Chi-restraints excluded: chain A residue 1096 HIS Chi-restraints excluded: chain G residue 887 THR Chi-restraints excluded: chain G residue 888 ILE Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 960 THR Chi-restraints excluded: chain G residue 1021 VAL Chi-restraints excluded: chain G residue 1042 PHE Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 914 TRP 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 960 THR Chi-restraints excluded: chain F residue 964 ILE Chi-restraints excluded: chain F residue 970 THR 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 1023 LEU Chi-restraints excluded: chain F residue 1034 HIS Chi-restraints excluded: chain F residue 1042 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1077 GLN Chi-restraints excluded: chain F residue 1084 ILE Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 887 THR 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 953 THR 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 1023 LEU Chi-restraints excluded: chain E residue 1042 PHE Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain E residue 1079 CYS Chi-restraints excluded: chain D residue 870 LEU Chi-restraints excluded: chain D residue 902 PHE Chi-restraints excluded: chain D residue 912 LEU 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 1023 LEU Chi-restraints excluded: chain D residue 1034 HIS Chi-restraints excluded: chain D residue 1042 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1096 HIS Chi-restraints excluded: chain C residue 887 THR 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 1023 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1088 PHE Chi-restraints excluded: chain C residue 1096 HIS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 927 LEU Chi-restraints excluded: chain B residue 930 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 435 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 391 optimal weight: 0.3980 chunk 299 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 429 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.191910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145431 restraints weight = 56247.837| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 4.57 r_work: 0.3521 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29099 Z= 0.140 Angle : 0.482 8.960 40131 Z= 0.267 Chirality : 0.039 0.160 5362 Planarity : 0.004 0.046 5432 Dihedral : 4.140 24.417 5068 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.79 % Allowed : 31.49 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.12), residues: 4865 helix: 2.83 (0.08), residues: 3542 sheet: -0.30 (0.30), residues: 329 loop : -2.06 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 944 TYR 0.009 0.001 TYR B 891 PHE 0.019 0.001 PHE F 931 TRP 0.015 0.001 TRP E 994 HIS 0.004 0.001 HIS A1094 Details of bonding type rmsd covalent geometry : bond 0.00277 (29099) covalent geometry : angle 0.48205 (40131) hydrogen bonds : bond 0.04172 ( 3005) hydrogen bonds : angle 3.76148 ( 8847) *********************** 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 602 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 543 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8249 (mt) cc_final: 0.7905 (mt) REVERT: A 925 PHE cc_start: 0.7446 (t80) cc_final: 0.7190 (t80) REVERT: A 995 SER cc_start: 0.8314 (t) cc_final: 0.8032 (p) REVERT: A 1063 ASP cc_start: 0.7288 (t0) cc_final: 0.6847 (t0) REVERT: G 925 PHE cc_start: 0.7813 (t80) cc_final: 0.7513 (t80) REVERT: G 1063 ASP cc_start: 0.7085 (t0) cc_final: 0.6760 (t0) REVERT: G 1079 CYS cc_start: 0.7998 (t) cc_final: 0.7704 (m) REVERT: F 889 LEU cc_start: 0.8297 (mt) cc_final: 0.7921 (mt) REVERT: F 1014 ASP cc_start: 0.8466 (t0) cc_final: 0.7727 (m-30) REVERT: F 1016 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7891 (mm-30) REVERT: F 1053 GLU cc_start: 0.8375 (tt0) cc_final: 0.8098 (tt0) REVERT: F 1076 ASP cc_start: 0.8420 (t0) cc_final: 0.8086 (t0) REVERT: F 1079 CYS cc_start: 0.8046 (t) cc_final: 0.7818 (m) REVERT: E 889 LEU cc_start: 0.8387 (mt) cc_final: 0.8001 (mt) REVERT: E 1063 ASP cc_start: 0.7316 (t0) cc_final: 0.7108 (t0) REVERT: E 1066 ARG cc_start: 0.7717 (mmp80) cc_final: 0.7447 (mmp-170) REVERT: D 889 LEU cc_start: 0.8279 (mt) cc_final: 0.7960 (mt) REVERT: D 1063 ASP cc_start: 0.7414 (t70) cc_final: 0.6961 (t70) REVERT: D 1077 GLN cc_start: 0.8365 (tp-100) cc_final: 0.8046 (tp40) REVERT: D 1079 CYS cc_start: 0.8316 (t) cc_final: 0.7780 (t) REVERT: D 1084 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7812 (pt) REVERT: C 888 ILE cc_start: 0.8031 (mm) cc_final: 0.7790 (mm) REVERT: C 889 LEU cc_start: 0.8331 (mt) cc_final: 0.8043 (mt) REVERT: C 892 ILE cc_start: 0.8613 (mm) cc_final: 0.8396 (mm) REVERT: C 944 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8083 (mtp180) REVERT: C 1015 LEU cc_start: 0.8737 (mt) cc_final: 0.8487 (mp) REVERT: C 1063 ASP cc_start: 0.7289 (t0) cc_final: 0.6791 (t0) REVERT: B 891 TYR cc_start: 0.8170 (m-80) cc_final: 0.7874 (m-80) REVERT: B 944 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8153 (mtp-110) REVERT: B 990 ARG cc_start: 0.8842 (mtt90) cc_final: 0.8636 (mtt-85) REVERT: B 995 SER cc_start: 0.8489 (t) cc_final: 0.8063 (p) REVERT: B 1031 ARG cc_start: 0.7439 (mmm160) cc_final: 0.6700 (mmm160) REVERT: B 1063 ASP cc_start: 0.7112 (t0) cc_final: 0.6468 (t0) outliers start: 59 outliers final: 48 residues processed: 580 average time/residue: 0.1709 time to fit residues: 157.6298 Evaluate side-chains 585 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 536 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 953 THR 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 938 LEU Chi-restraints excluded: chain G residue 953 THR Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 892 ILE Chi-restraints excluded: chain F residue 894 ILE 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 1084 ILE Chi-restraints excluded: chain F residue 1096 HIS Chi-restraints excluded: chain E residue 894 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 966 ILE Chi-restraints excluded: chain E residue 1007 LEU Chi-restraints excluded: chain E residue 1009 VAL Chi-restraints excluded: chain E residue 1049 THR Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 894 ILE Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ILE 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 1007 LEU Chi-restraints excluded: chain C residue 1022 LEU 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 930 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 1007 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 435 optimal weight: 20.0000 chunk 62 optimal weight: 0.0040 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 444 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 0.0020 chunk 469 optimal weight: 0.9990 chunk 494 optimal weight: 0.7980 chunk 417 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1082 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.188628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146045 restraints weight = 59310.279| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.14 r_work: 0.3662 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29099 Z= 0.134 Angle : 0.458 9.631 40131 Z= 0.253 Chirality : 0.039 0.188 5362 Planarity : 0.003 0.045 5432 Dihedral : 3.840 24.114 5068 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.19 % Allowed : 31.25 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.12), residues: 4865 helix: 3.25 (0.08), residues: 3556 sheet: -0.18 (0.30), residues: 329 loop : -1.98 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G1031 TYR 0.018 0.001 TYR C 891 PHE 0.014 0.001 PHE D1045 TRP 0.010 0.001 TRP F 914 HIS 0.005 0.001 HIS D1096 Details of bonding type rmsd covalent geometry : bond 0.00281 (29099) covalent geometry : angle 0.45837 (40131) hydrogen bonds : bond 0.03813 ( 3005) hydrogen bonds : angle 3.43943 ( 8847) *********************** 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 614 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 550 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8255 (mt) cc_final: 0.7891 (mt) REVERT: A 925 PHE cc_start: 0.7468 (t80) cc_final: 0.7229 (t80) REVERT: A 995 SER cc_start: 0.8228 (t) cc_final: 0.7951 (p) REVERT: A 1014 ASP cc_start: 0.8391 (t0) cc_final: 0.7668 (m-30) REVERT: A 1063 ASP cc_start: 0.7188 (t0) cc_final: 0.6712 (t0) REVERT: G 925 PHE cc_start: 0.7778 (t80) cc_final: 0.7496 (t80) REVERT: G 995 SER cc_start: 0.8291 (t) cc_final: 0.7969 (p) REVERT: G 1063 ASP cc_start: 0.6946 (t0) cc_final: 0.6637 (t0) REVERT: G 1079 CYS cc_start: 0.7898 (t) cc_final: 0.7644 (m) REVERT: G 1082 ASN cc_start: 0.8115 (m110) cc_final: 0.7797 (m110) REVERT: F 889 LEU cc_start: 0.8185 (mt) cc_final: 0.7861 (mt) REVERT: F 1031 ARG cc_start: 0.7475 (mmm-85) cc_final: 0.7049 (mmm160) REVERT: F 1053 GLU cc_start: 0.8279 (tt0) cc_final: 0.7974 (tt0) REVERT: F 1063 ASP cc_start: 0.7055 (t0) cc_final: 0.6595 (t0) REVERT: F 1076 ASP cc_start: 0.8437 (t0) cc_final: 0.8077 (t0) REVERT: F 1079 CYS cc_start: 0.8048 (t) cc_final: 0.7797 (m) REVERT: E 889 LEU cc_start: 0.8295 (mt) cc_final: 0.7919 (mt) REVERT: E 890 ASN cc_start: 0.8495 (m-40) cc_final: 0.8229 (m110) REVERT: E 995 SER cc_start: 0.8292 (t) cc_final: 0.8035 (t) REVERT: E 1063 ASP cc_start: 0.7439 (t0) cc_final: 0.7033 (t0) REVERT: D 889 LEU cc_start: 0.8274 (mt) cc_final: 0.7976 (mt) REVERT: D 984 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8586 (mtmm) REVERT: D 1063 ASP cc_start: 0.7288 (t70) cc_final: 0.6885 (t70) REVERT: D 1077 GLN cc_start: 0.8300 (tp-100) cc_final: 0.7942 (tp40) REVERT: D 1079 CYS cc_start: 0.8277 (t) cc_final: 0.7736 (t) REVERT: D 1084 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7767 (pt) REVERT: C 888 ILE cc_start: 0.7953 (mm) cc_final: 0.7687 (mm) REVERT: C 889 LEU cc_start: 0.8225 (mt) cc_final: 0.7931 (mt) REVERT: C 892 ILE cc_start: 0.8493 (mm) cc_final: 0.8254 (mm) REVERT: C 944 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8020 (mtp180) REVERT: C 995 SER cc_start: 0.8278 (t) cc_final: 0.7997 (p) REVERT: C 1015 LEU cc_start: 0.8720 (mt) cc_final: 0.8486 (mp) REVERT: C 1063 ASP cc_start: 0.7135 (t0) cc_final: 0.6595 (t0) REVERT: C 1088 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: B 891 TYR cc_start: 0.7897 (m-80) cc_final: 0.7682 (m-80) REVERT: B 934 PHE cc_start: 0.7798 (t80) cc_final: 0.7575 (t80) REVERT: B 944 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8130 (mtp180) REVERT: B 990 ARG cc_start: 0.8813 (mtt90) cc_final: 0.8595 (mtt-85) REVERT: B 995 SER cc_start: 0.8434 (t) cc_final: 0.8022 (p) REVERT: B 1031 ARG cc_start: 0.7372 (mmm160) cc_final: 0.6631 (mmm160) REVERT: B 1063 ASP cc_start: 0.7012 (t0) cc_final: 0.6327 (t0) REVERT: B 1083 ASP cc_start: 0.8457 (t0) cc_final: 0.8228 (t0) outliers start: 64 outliers final: 45 residues processed: 597 average time/residue: 0.1725 time to fit residues: 163.6870 Evaluate side-chains 587 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 540 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 912 LEU 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 1079 CYS 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 964 ILE Chi-restraints excluded: chain G residue 1056 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 960 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 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 1056 LEU Chi-restraints excluded: chain E residue 1091 LEU Chi-restraints excluded: chain E residue 1096 HIS Chi-restraints excluded: chain D residue 912 LEU 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 1084 ILE 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 953 THR 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 C residue 1096 HIS 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 967 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL 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 352 optimal weight: 0.5980 chunk 445 optimal weight: 30.0000 chunk 200 optimal weight: 0.0170 chunk 311 optimal weight: 10.0000 chunk 452 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 474 optimal weight: 0.0870 chunk 354 optimal weight: 0.0570 chunk 489 optimal weight: 0.8980 chunk 142 optimal weight: 30.0000 chunk 418 optimal weight: 0.6980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1082 ASN F 890 ASN F1082 ASN F1089 ASN E1082 ASN C 890 ASN B1082 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.193408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.156512 restraints weight = 64266.146| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 4.88 r_work: 0.3624 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2151 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= 0.100 Angle : 0.439 8.697 40131 Z= 0.239 Chirality : 0.039 0.194 5362 Planarity : 0.003 0.051 5432 Dihedral : 3.638 22.862 5068 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.87 % Allowed : 32.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.12), residues: 4865 helix: 3.42 (0.08), residues: 3556 sheet: -0.03 (0.30), residues: 329 loop : -2.02 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1031 TYR 0.012 0.001 TYR B 891 PHE 0.030 0.001 PHE E 925 TRP 0.008 0.000 TRP F 914 HIS 0.003 0.001 HIS A1094 Details of bonding type rmsd covalent geometry : bond 0.00190 (29099) covalent geometry : angle 0.43895 (40131) hydrogen bonds : bond 0.03446 ( 3005) hydrogen bonds : angle 3.25792 ( 8847) *********************** 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 616 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 556 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8269 (mt) cc_final: 0.7915 (mt) REVERT: A 925 PHE cc_start: 0.7432 (t80) cc_final: 0.7196 (t80) REVERT: A 995 SER cc_start: 0.8220 (t) cc_final: 0.7970 (p) REVERT: A 1014 ASP cc_start: 0.8276 (t0) cc_final: 0.7542 (m-30) REVERT: A 1063 ASP cc_start: 0.7023 (t0) cc_final: 0.6555 (t0) REVERT: G 925 PHE cc_start: 0.7712 (t80) cc_final: 0.7432 (t80) REVERT: G 995 SER cc_start: 0.8213 (t) cc_final: 0.7887 (p) REVERT: G 1063 ASP cc_start: 0.6795 (t0) cc_final: 0.6482 (t0) REVERT: G 1079 CYS cc_start: 0.7860 (t) cc_final: 0.7637 (m) REVERT: G 1082 ASN cc_start: 0.8031 (m-40) cc_final: 0.7744 (m110) REVERT: F 889 LEU cc_start: 0.8140 (mt) cc_final: 0.7843 (mt) REVERT: F 1031 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.7113 (mmm160) REVERT: F 1053 GLU cc_start: 0.8259 (tt0) cc_final: 0.7985 (tt0) REVERT: F 1063 ASP cc_start: 0.6852 (t0) cc_final: 0.6386 (t0) REVERT: F 1076 ASP cc_start: 0.8523 (t0) cc_final: 0.8280 (t0) REVERT: F 1079 CYS cc_start: 0.8120 (t) cc_final: 0.7831 (m) REVERT: E 889 LEU cc_start: 0.8251 (mt) cc_final: 0.7883 (mt) REVERT: E 995 SER cc_start: 0.8177 (t) cc_final: 0.7622 (p) REVERT: E 1083 ASP cc_start: 0.8687 (t0) cc_final: 0.8365 (t0) REVERT: E 1088 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: E 1093 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8680 (m) REVERT: D 889 LEU cc_start: 0.8260 (mt) cc_final: 0.7961 (mt) REVERT: D 890 ASN cc_start: 0.8355 (m-40) cc_final: 0.8085 (m110) REVERT: D 984 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8669 (mtmm) REVERT: D 1063 ASP cc_start: 0.7052 (t70) cc_final: 0.6772 (t70) REVERT: D 1077 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7993 (tp40) REVERT: D 1079 CYS cc_start: 0.8322 (t) cc_final: 0.7809 (t) REVERT: D 1084 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7818 (pt) REVERT: C 889 LEU cc_start: 0.8199 (mt) cc_final: 0.7920 (mt) REVERT: C 890 ASN cc_start: 0.8335 (m-40) cc_final: 0.8088 (m110) REVERT: C 892 ILE cc_start: 0.8594 (mm) cc_final: 0.8352 (mm) REVERT: C 944 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7814 (mtm180) REVERT: C 995 SER cc_start: 0.8253 (t) cc_final: 0.7993 (p) REVERT: C 1015 LEU cc_start: 0.8701 (mt) cc_final: 0.8470 (mp) REVERT: C 1022 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7829 (mp) REVERT: C 1063 ASP cc_start: 0.6935 (t0) cc_final: 0.6419 (t0) REVERT: B 891 TYR cc_start: 0.8033 (m-80) cc_final: 0.7764 (m-80) REVERT: B 934 PHE cc_start: 0.7805 (t80) cc_final: 0.7344 (t80) REVERT: B 944 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8025 (mtp180) REVERT: B 995 SER cc_start: 0.8383 (t) cc_final: 0.8005 (p) REVERT: B 1031 ARG cc_start: 0.7384 (mmm160) cc_final: 0.6726 (mmm160) REVERT: B 1063 ASP cc_start: 0.6851 (t0) cc_final: 0.6211 (t0) REVERT: B 1083 ASP cc_start: 0.8549 (t0) cc_final: 0.8288 (t0) outliers start: 60 outliers final: 44 residues processed: 602 average time/residue: 0.1711 time to fit residues: 163.8352 Evaluate side-chains 598 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 550 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE 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 1079 CYS Chi-restraints excluded: chain G residue 927 LEU Chi-restraints excluded: chain G residue 938 LEU Chi-restraints excluded: chain G residue 1007 LEU Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain G residue 1096 HIS Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 960 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 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 1007 LEU Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain E residue 1088 PHE 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 D residue 1084 ILE 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 1007 LEU Chi-restraints excluded: chain C residue 1022 LEU 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 938 LEU Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL 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 454 optimal weight: 0.0980 chunk 42 optimal weight: 2.9990 chunk 332 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 458 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 345 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 401 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1089 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.194240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154707 restraints weight = 58470.046| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.43 r_work: 0.3606 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29099 Z= 0.145 Angle : 0.466 9.765 40131 Z= 0.256 Chirality : 0.039 0.212 5362 Planarity : 0.003 0.049 5432 Dihedral : 3.682 23.326 5068 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.46 % Allowed : 32.71 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.12), residues: 4865 helix: 3.55 (0.08), residues: 3521 sheet: -0.05 (0.30), residues: 329 loop : -1.81 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1031 TYR 0.007 0.001 TYR C 891 PHE 0.025 0.001 PHE C 934 TRP 0.006 0.000 TRP E 994 HIS 0.005 0.001 HIS F1096 Details of bonding type rmsd covalent geometry : bond 0.00311 (29099) covalent geometry : angle 0.46560 (40131) hydrogen bonds : bond 0.03697 ( 3005) hydrogen bonds : angle 3.30449 ( 8847) *********************** 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 610 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 555 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8262 (mt) cc_final: 0.7906 (mt) REVERT: A 925 PHE cc_start: 0.7407 (t80) cc_final: 0.7178 (t80) REVERT: A 995 SER cc_start: 0.8210 (t) cc_final: 0.7954 (p) REVERT: A 1063 ASP cc_start: 0.7150 (t0) cc_final: 0.6637 (t0) REVERT: G 925 PHE cc_start: 0.7729 (t80) cc_final: 0.7450 (t80) REVERT: G 995 SER cc_start: 0.8305 (t) cc_final: 0.7968 (p) REVERT: G 1063 ASP cc_start: 0.6972 (t0) cc_final: 0.6607 (t0) REVERT: G 1079 CYS cc_start: 0.7818 (t) cc_final: 0.7551 (m) REVERT: G 1082 ASN cc_start: 0.7988 (m-40) cc_final: 0.7765 (m110) REVERT: F 889 LEU cc_start: 0.8183 (mt) cc_final: 0.7894 (mt) REVERT: F 1031 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7086 (mmm160) REVERT: F 1053 GLU cc_start: 0.8241 (tt0) cc_final: 0.7978 (tt0) REVERT: F 1063 ASP cc_start: 0.7076 (t0) cc_final: 0.6563 (t0) REVERT: F 1076 ASP cc_start: 0.8497 (t0) cc_final: 0.8270 (t0) REVERT: F 1079 CYS cc_start: 0.8122 (t) cc_final: 0.7829 (m) REVERT: E 889 LEU cc_start: 0.8220 (mt) cc_final: 0.7855 (mt) REVERT: E 995 SER cc_start: 0.8129 (t) cc_final: 0.7858 (t) REVERT: E 1083 ASP cc_start: 0.8658 (t0) cc_final: 0.8358 (t0) REVERT: E 1093 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8657 (m) REVERT: D 889 LEU cc_start: 0.8277 (mt) cc_final: 0.8002 (mt) REVERT: D 984 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8632 (mtmm) REVERT: D 1063 ASP cc_start: 0.7122 (t70) cc_final: 0.6823 (t70) REVERT: D 1077 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7991 (tp40) REVERT: D 1079 CYS cc_start: 0.8275 (t) cc_final: 0.7769 (t) REVERT: D 1084 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7760 (pt) REVERT: C 889 LEU cc_start: 0.8260 (mt) cc_final: 0.7977 (mt) REVERT: C 890 ASN cc_start: 0.8369 (m-40) cc_final: 0.8115 (m110) REVERT: C 892 ILE cc_start: 0.8541 (mm) cc_final: 0.8302 (mm) REVERT: C 944 ARG cc_start: 0.8381 (mtp85) cc_final: 0.7910 (mtm180) REVERT: C 995 SER cc_start: 0.8296 (t) cc_final: 0.8031 (p) REVERT: C 1022 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7851 (mp) REVERT: C 1063 ASP cc_start: 0.7083 (t0) cc_final: 0.6536 (t0) REVERT: C 1080 ARG cc_start: 0.8531 (ttm110) cc_final: 0.8140 (ptp-110) REVERT: B 891 TYR cc_start: 0.7979 (m-80) cc_final: 0.7773 (m-80) REVERT: B 944 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8109 (mtp180) REVERT: B 995 SER cc_start: 0.8402 (t) cc_final: 0.8014 (p) REVERT: B 1031 ARG cc_start: 0.7421 (mmm160) cc_final: 0.6727 (mmm160) REVERT: B 1063 ASP cc_start: 0.6981 (t0) cc_final: 0.6378 (t0) REVERT: B 1083 ASP cc_start: 0.8533 (t0) cc_final: 0.8300 (t0) outliers start: 55 outliers final: 44 residues processed: 595 average time/residue: 0.1693 time to fit residues: 160.9964 Evaluate side-chains 595 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 548 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 885 ILE 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 1007 LEU Chi-restraints excluded: chain A residue 1079 CYS 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 964 ILE Chi-restraints excluded: chain G residue 1007 LEU Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain G residue 1096 HIS 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 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 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 D residue 1084 ILE 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 1022 LEU Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1096 HIS Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 939 ILE Chi-restraints excluded: chain B residue 942 PHE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1021 VAL 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 335 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 444 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 346 optimal weight: 0.4980 chunk 38 optimal weight: 20.0000 chunk 433 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 355 optimal weight: 30.0000 chunk 373 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.187026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139761 restraints weight = 55802.007| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 5.04 r_work: 0.3410 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 29099 Z= 0.445 Angle : 0.700 12.202 40131 Z= 0.402 Chirality : 0.047 0.217 5362 Planarity : 0.005 0.063 5432 Dihedral : 4.756 25.675 5068 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.03 % Allowed : 33.52 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.12), residues: 4865 helix: 2.39 (0.09), residues: 3507 sheet: -0.39 (0.30), residues: 315 loop : -2.23 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G1031 TYR 0.021 0.003 TYR F 891 PHE 0.056 0.003 PHE F1042 TRP 0.013 0.001 TRP D 994 HIS 0.016 0.004 HIS C1096 Details of bonding type rmsd covalent geometry : bond 0.00979 (29099) covalent geometry : angle 0.70019 (40131) hydrogen bonds : bond 0.05757 ( 3005) hydrogen bonds : angle 4.43802 ( 8847) *********************** 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 608 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 546 time to evaluate : 0.976 Fit side-chains REVERT: A 889 LEU cc_start: 0.8403 (mt) cc_final: 0.8144 (mt) REVERT: A 925 PHE cc_start: 0.7604 (t80) cc_final: 0.7339 (t80) REVERT: A 995 SER cc_start: 0.8475 (t) cc_final: 0.8162 (p) REVERT: A 1014 ASP cc_start: 0.8632 (t0) cc_final: 0.7930 (m-30) REVERT: A 1063 ASP cc_start: 0.7648 (t0) cc_final: 0.7135 (t0) REVERT: G 893 ILE cc_start: 0.8801 (mm) cc_final: 0.8562 (mm) REVERT: G 1063 ASP cc_start: 0.7521 (t0) cc_final: 0.7181 (t0) REVERT: G 1079 CYS cc_start: 0.7953 (t) cc_final: 0.7642 (m) REVERT: F 889 LEU cc_start: 0.8437 (mt) cc_final: 0.8161 (mt) REVERT: F 1014 ASP cc_start: 0.8525 (t0) cc_final: 0.7849 (m-30) REVERT: F 1063 ASP cc_start: 0.7590 (t0) cc_final: 0.7320 (t0) REVERT: F 1076 ASP cc_start: 0.8438 (t0) cc_final: 0.8190 (t0) REVERT: E 889 LEU cc_start: 0.8284 (mt) cc_final: 0.7987 (mt) REVERT: E 1063 ASP cc_start: 0.8031 (t70) cc_final: 0.7757 (t70) REVERT: D 889 LEU cc_start: 0.8394 (mt) cc_final: 0.8079 (mt) REVERT: D 984 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8643 (mtmm) REVERT: D 1063 ASP cc_start: 0.7697 (t70) cc_final: 0.7187 (t70) REVERT: D 1077 GLN cc_start: 0.8338 (tp-100) cc_final: 0.8000 (tp40) REVERT: D 1084 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (pt) REVERT: C 888 ILE cc_start: 0.8129 (mm) cc_final: 0.7889 (mm) REVERT: C 889 LEU cc_start: 0.8424 (mt) cc_final: 0.8108 (mt) REVERT: C 892 ILE cc_start: 0.8696 (mm) cc_final: 0.8458 (mm) REVERT: C 944 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7962 (mtm180) REVERT: C 1022 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7859 (mp) REVERT: C 1063 ASP cc_start: 0.7624 (t0) cc_final: 0.7046 (t0) REVERT: C 1080 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8179 (ptp-110) REVERT: B 891 TYR cc_start: 0.8217 (m-80) cc_final: 0.7950 (m-80) REVERT: B 995 SER cc_start: 0.8612 (t) cc_final: 0.8173 (p) REVERT: B 1014 ASP cc_start: 0.8612 (t0) cc_final: 0.7888 (m-30) REVERT: B 1020 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7427 (ptpt) REVERT: B 1031 ARG cc_start: 0.7734 (mmm160) cc_final: 0.6865 (mmm160) REVERT: B 1063 ASP cc_start: 0.7477 (t0) cc_final: 0.6893 (t0) REVERT: B 1083 ASP cc_start: 0.8495 (t0) cc_final: 0.8284 (t0) outliers start: 62 outliers final: 48 residues processed: 587 average time/residue: 0.1733 time to fit residues: 160.3868 Evaluate side-chains 592 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 541 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 953 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1079 CYS 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 960 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain G residue 1056 LEU Chi-restraints excluded: chain F residue 927 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 960 THR 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 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 1007 LEU Chi-restraints excluded: chain E residue 1056 LEU Chi-restraints excluded: chain D residue 912 LEU 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 1056 LEU Chi-restraints excluded: chain D residue 1084 ILE 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 1021 VAL Chi-restraints excluded: chain C residue 1022 LEU 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 938 LEU Chi-restraints excluded: chain B residue 939 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1020 LYS Chi-restraints excluded: chain B residue 1021 VAL 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 32 optimal weight: 6.9990 chunk 197 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 496 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 448 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 890 ASN E1082 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.189412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141893 restraints weight = 55997.662| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 4.27 r_work: 0.3473 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29099 Z= 0.240 Angle : 0.543 9.463 40131 Z= 0.304 Chirality : 0.042 0.212 5362 Planarity : 0.004 0.050 5432 Dihedral : 4.244 25.173 5068 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.06 % Allowed : 34.66 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.12), residues: 4865 helix: 2.86 (0.08), residues: 3535 sheet: -0.07 (0.35), residues: 259 loop : -2.17 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1031 TYR 0.010 0.002 TYR D 891 PHE 0.027 0.002 PHE C 934 TRP 0.011 0.001 TRP E 994 HIS 0.007 0.002 HIS C1096 Details of bonding type rmsd covalent geometry : bond 0.00522 (29099) covalent geometry : angle 0.54323 (40131) hydrogen bonds : bond 0.04500 ( 3005) hydrogen bonds : angle 3.85286 ( 8847) ********************** 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 594 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 544 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 889 LEU cc_start: 0.8286 (mt) cc_final: 0.7944 (mt) REVERT: A 925 PHE cc_start: 0.7477 (t80) cc_final: 0.7220 (t80) REVERT: A 995 SER cc_start: 0.8352 (t) cc_final: 0.8051 (p) REVERT: A 1014 ASP cc_start: 0.8490 (t0) cc_final: 0.7694 (m-30) REVERT: A 1015 LEU cc_start: 0.8815 (mt) cc_final: 0.8422 (mp) REVERT: A 1063 ASP cc_start: 0.7375 (t0) cc_final: 0.6870 (t0) REVERT: G 893 ILE cc_start: 0.8866 (mm) cc_final: 0.8638 (mm) REVERT: G 992 ILE cc_start: 0.8548 (mm) cc_final: 0.8256 (mt) REVERT: G 1063 ASP cc_start: 0.7211 (t0) cc_final: 0.6904 (t0) REVERT: F 889 LEU cc_start: 0.8366 (mt) cc_final: 0.8098 (mt) REVERT: F 1031 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7141 (mmm160) REVERT: F 1053 GLU cc_start: 0.8392 (tt0) cc_final: 0.8153 (tt0) REVERT: F 1063 ASP cc_start: 0.7386 (t0) cc_final: 0.6909 (t0) REVERT: F 1076 ASP cc_start: 0.8441 (t0) cc_final: 0.8112 (t0) REVERT: E 889 LEU cc_start: 0.8196 (mt) cc_final: 0.7860 (mt) REVERT: D 889 LEU cc_start: 0.8363 (mt) cc_final: 0.8089 (mt) REVERT: D 984 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8693 (mtmm) REVERT: D 1063 ASP cc_start: 0.7527 (t70) cc_final: 0.7092 (t70) REVERT: D 1077 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8051 (tp40) REVERT: D 1084 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7859 (pt) REVERT: C 888 ILE cc_start: 0.8062 (mm) cc_final: 0.7832 (mm) REVERT: C 889 LEU cc_start: 0.8342 (mt) cc_final: 0.8039 (mt) REVERT: C 892 ILE cc_start: 0.8626 (mm) cc_final: 0.8388 (mm) REVERT: C 1022 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7863 (mp) REVERT: C 1063 ASP cc_start: 0.7420 (t0) cc_final: 0.6839 (t0) REVERT: C 1080 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8200 (ptp-110) REVERT: B 891 TYR cc_start: 0.8201 (m-80) cc_final: 0.7962 (m-80) REVERT: B 995 SER cc_start: 0.8487 (t) cc_final: 0.8055 (p) REVERT: B 1031 ARG cc_start: 0.7655 (mmm160) cc_final: 0.6897 (mmm160) REVERT: B 1063 ASP cc_start: 0.7302 (t0) cc_final: 0.6616 (t0) REVERT: B 1083 ASP cc_start: 0.8476 (t0) cc_final: 0.8210 (t0) outliers start: 50 outliers final: 45 residues processed: 580 average time/residue: 0.1763 time to fit residues: 162.7290 Evaluate side-chains 591 residues out of total 4403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 544 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 953 THR Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1079 CYS 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 960 THR Chi-restraints excluded: chain G residue 964 ILE Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 960 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 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 1096 HIS Chi-restraints excluded: chain D residue 894 ILE Chi-restraints excluded: chain D residue 912 LEU 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 1034 HIS Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1084 ILE 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 1022 LEU 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 938 LEU Chi-restraints excluded: chain B residue 939 ILE Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 1007 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 190 optimal weight: 1.9990 chunk 456 optimal weight: 5.9990 chunk 283 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 344 optimal weight: 1.9990 chunk 351 optimal weight: 0.8980 chunk 481 optimal weight: 0.9980 chunk 415 optimal weight: 0.9990 chunk 280 optimal weight: 0.7980 chunk 458 optimal weight: 5.9990 chunk 454 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1082 ASN F 890 ASN F1082 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.193635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154467 restraints weight = 58927.058| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.71 r_work: 0.3570 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29099 Z= 0.139 Angle : 0.479 9.579 40131 Z= 0.264 Chirality : 0.040 0.213 5362 Planarity : 0.003 0.054 5432 Dihedral : 3.898 24.301 5068 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.25 % Allowed : 35.31 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.12), residues: 4865 helix: 3.27 (0.08), residues: 3556 sheet: -0.12 (0.30), residues: 329 loop : -2.01 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G1031 TYR 0.012 0.001 TYR C 891 PHE 0.029 0.001 PHE C 934 TRP 0.008 0.001 TRP F 914 HIS 0.005 0.001 HIS A1094 Details of bonding type rmsd covalent geometry : bond 0.00290 (29099) covalent geometry : angle 0.47918 (40131) hydrogen bonds : bond 0.03778 ( 3005) hydrogen bonds : angle 3.45760 ( 8847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8619.57 seconds wall clock time: 146 minutes 40.32 seconds (8800.32 seconds total)