Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 11:07:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux1_26845/10_2023/7ux1_26845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux1_26845/10_2023/7ux1_26845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux1_26845/10_2023/7ux1_26845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux1_26845/10_2023/7ux1_26845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux1_26845/10_2023/7ux1_26845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ux1_26845/10_2023/7ux1_26845.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 17857 2.51 5 N 5523 2.21 5 O 5530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 28931 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "G" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "F" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "E" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "D" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "C" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Chain: "B" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 4133 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 14, 'TRANS': 698} Chain breaks: 8 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2182 Unresolved non-hydrogen dihedrals: 1407 Unresolved non-hydrogen chiralities: 184 Planarities with less than four sites: {'GLN:plan1': 39, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 25, 'TRP:plan': 18, 'ASP:plan': 16, 'PHE:plan': 20, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 892 Time building chain proxies: 16.47, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 12.83 Conformation dependent library (CDL) restraints added in 5.8 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: 2.98 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: 12.33 Time building geometry restraints manager: 13.76 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: 100.76 - 107.42: 451 107.42 - 114.07: 17143 114.07 - 120.73: 13218 120.73 - 127.39: 9207 127.39 - 134.04: 112 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 2.440 nonbonded pdb=" O SER G 956 " pdb=" OG SER G 956 " model vdw 2.261 2.440 nonbonded pdb=" O SER D 956 " pdb=" OG SER D 956 " model vdw 2.261 2.440 nonbonded pdb=" O SER C 956 " pdb=" OG SER C 956 " model vdw 2.261 2.440 nonbonded pdb=" O SER E 956 " pdb=" OG SER E 956 " model vdw 2.261 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 3.290 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: 14.530 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 80.400 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.410 ------------------------------------------------------------------------------- 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= 0.195 Angle : 0.560 9.482 40131 Z= 0.344 Chirality : 0.041 0.222 5362 Planarity : 0.003 0.048 5432 Dihedral : 12.464 89.636 7581 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 29.79 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.13), residues: 4865 helix: 3.23 (0.08), residues: 3556 sheet: -0.34 (0.29), residues: 357 loop : -1.56 (0.21), residues: 952 *********************** 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 fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 3.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 563 average time/residue: 0.3788 time to fit residues: 339.1280 Evaluate side-chains 541 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 419 optimal weight: 1.9990 chunk 376 optimal weight: 20.0000 chunk 209 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 389 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 236 optimal weight: 20.0000 chunk 289 optimal weight: 8.9990 chunk 451 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1096 HIS G1096 HIS F1052 HIS F1082 ASN F1096 HIS E1096 HIS D1096 HIS C1096 HIS B1082 ASN B1096 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 29099 Z= 0.414 Angle : 0.531 8.911 40131 Z= 0.302 Chirality : 0.042 0.165 5362 Planarity : 0.004 0.053 5432 Dihedral : 4.047 25.485 5068 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.74 % Allowed : 27.44 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.13), residues: 4865 helix: 3.10 (0.08), residues: 3563 sheet: -0.11 (0.30), residues: 329 loop : -1.78 (0.20), residues: 973 *********************** 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 627 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 544 time to evaluate : 2.975 Fit side-chains outliers start: 83 outliers final: 62 residues processed: 596 average time/residue: 0.3897 time to fit residues: 370.5771 Evaluate side-chains 595 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 533 time to evaluate : 3.226 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.2538 time to fit residues: 34.3847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 250 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 375 optimal weight: 7.9990 chunk 307 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 452 optimal weight: 7.9990 chunk 488 optimal weight: 1.9990 chunk 402 optimal weight: 3.9990 chunk 448 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 362 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 993 ASN F1082 ASN E1052 HIS C1052 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.091 29099 Z= 0.712 Angle : 0.693 10.900 40131 Z= 0.400 Chirality : 0.047 0.218 5362 Planarity : 0.005 0.068 5432 Dihedral : 4.727 24.191 5068 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 6.33 % Allowed : 28.08 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.12), residues: 4865 helix: 2.28 (0.09), residues: 3507 sheet: -0.23 (0.30), residues: 315 loop : -1.96 (0.18), residues: 1043 *********************** 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 615 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 537 time to evaluate : 3.200 Fit side-chains outliers start: 78 outliers final: 52 residues processed: 602 average time/residue: 0.3818 time to fit residues: 367.3597 Evaluate side-chains 578 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 526 time to evaluate : 3.014 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2452 time to fit residues: 29.0570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 446 optimal weight: 9.9990 chunk 339 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 453 optimal weight: 6.9990 chunk 480 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 993 ASN F1082 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29099 Z= 0.380 Angle : 0.537 8.524 40131 Z= 0.302 Chirality : 0.041 0.176 5362 Planarity : 0.004 0.050 5432 Dihedral : 4.296 24.738 5068 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.38 % Allowed : 30.28 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.12), residues: 4865 helix: 2.74 (0.09), residues: 3528 sheet: -0.18 (0.30), residues: 329 loop : -1.95 (0.18), residues: 1008 *********************** 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 591 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 537 time to evaluate : 3.165 Fit side-chains outliers start: 54 outliers final: 33 residues processed: 569 average time/residue: 0.3905 time to fit residues: 354.8927 Evaluate side-chains 564 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 531 time to evaluate : 3.076 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2414 time to fit residues: 19.4678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 400 optimal weight: 9.9990 chunk 272 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 357 optimal weight: 7.9990 chunk 198 optimal weight: 0.6980 chunk 409 optimal weight: 0.9980 chunk 332 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 245 optimal weight: 3.9990 chunk 431 optimal weight: 0.0040 chunk 121 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1082 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29099 Z= 0.223 Angle : 0.472 7.658 40131 Z= 0.261 Chirality : 0.039 0.175 5362 Planarity : 0.003 0.045 5432 Dihedral : 3.958 23.978 5068 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.17 % Allowed : 31.74 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.12), residues: 4865 helix: 3.17 (0.08), residues: 3542 sheet: -0.05 (0.30), residues: 329 loop : -1.84 (0.19), residues: 994 *********************** 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 571 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 532 time to evaluate : 3.041 Fit side-chains outliers start: 39 outliers final: 17 residues processed: 562 average time/residue: 0.3830 time to fit residues: 342.1748 Evaluate side-chains 543 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 526 time to evaluate : 3.476 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2500 time to fit residues: 13.0517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 161 optimal weight: 0.0070 chunk 432 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 282 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 chunk 480 optimal weight: 0.9980 chunk 399 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 39 optimal weight: 50.0000 chunk 159 optimal weight: 7.9990 chunk 252 optimal weight: 20.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G1082 ASN F1082 ASN E1082 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29099 Z= 0.175 Angle : 0.452 9.598 40131 Z= 0.248 Chirality : 0.039 0.188 5362 Planarity : 0.003 0.044 5432 Dihedral : 3.763 22.957 5068 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.87 % Allowed : 34.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.13), residues: 4865 helix: 3.39 (0.08), residues: 3556 sheet: 0.06 (0.30), residues: 329 loop : -1.75 (0.19), residues: 980 *********************** 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 550 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 527 time to evaluate : 2.873 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 542 average time/residue: 0.4026 time to fit residues: 344.5000 Evaluate side-chains 534 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 521 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2402 time to fit residues: 10.3630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 463 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 351 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 404 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 479 optimal weight: 4.9990 chunk 299 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29099 Z= 0.289 Angle : 0.496 8.442 40131 Z= 0.274 Chirality : 0.040 0.199 5362 Planarity : 0.003 0.047 5432 Dihedral : 3.870 23.556 5068 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.38 % Allowed : 35.47 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.12), residues: 4865 helix: 3.34 (0.08), residues: 3556 sheet: -0.08 (0.30), residues: 336 loop : -1.75 (0.19), residues: 973 *********************** 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 554 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 537 time to evaluate : 3.194 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 549 average time/residue: 0.4059 time to fit residues: 352.2833 Evaluate side-chains 541 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 531 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3005 time to fit residues: 9.4877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 296 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 376 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.243 29099 Z= 1.928 Angle : 1.334 20.775 40131 Z= 0.785 Chirality : 0.084 0.439 5362 Planarity : 0.011 0.103 5432 Dihedral : 7.227 35.354 5068 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.23 % Favored : 90.20 % Rotamer: Outliers : 6.41 % Allowed : 31.49 % Favored : 62.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4865 helix: -0.41 (0.08), residues: 3465 sheet: -1.24 (0.30), residues: 245 loop : -2.70 (0.18), residues: 1155 *********************** 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 612 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 533 time to evaluate : 3.411 Fit side-chains outliers start: 79 outliers final: 53 residues processed: 577 average time/residue: 0.3886 time to fit residues: 356.4655 Evaluate side-chains 581 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 528 time to evaluate : 3.266 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2501 time to fit residues: 29.1842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 435 optimal weight: 9.9990 chunk 458 optimal weight: 4.9990 chunk 418 optimal weight: 0.8980 chunk 446 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 194 optimal weight: 0.0670 chunk 350 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 403 optimal weight: 8.9990 chunk 422 optimal weight: 0.9980 chunk 444 optimal weight: 10.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1085 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29099 Z= 0.226 Angle : 0.566 9.443 40131 Z= 0.317 Chirality : 0.041 0.180 5362 Planarity : 0.004 0.063 5432 Dihedral : 4.822 24.079 5068 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.89 % Allowed : 34.58 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 4865 helix: 1.64 (0.09), residues: 3521 sheet: -0.45 (0.30), residues: 315 loop : -2.52 (0.17), residues: 1029 *********************** 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 541 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 530 time to evaluate : 3.022 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 537 average time/residue: 0.4014 time to fit residues: 342.7706 Evaluate side-chains 531 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 523 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3299 time to fit residues: 9.3199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 293 optimal weight: 9.9990 chunk 472 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 30.0000 chunk 328 optimal weight: 0.9980 chunk 495 optimal weight: 1.9990 chunk 455 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.100 29099 Z= 0.757 Angle : 0.752 10.973 40131 Z= 0.435 Chirality : 0.048 0.228 5362 Planarity : 0.006 0.068 5432 Dihedral : 5.319 25.322 5068 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 0.57 % Allowed : 37.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.12), residues: 4865 helix: 1.28 (0.09), residues: 3549 sheet: -0.67 (0.30), residues: 315 loop : -2.62 (0.18), residues: 1001 ********************** 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 531 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 524 time to evaluate : 3.308 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 528 average time/residue: 0.4067 time to fit residues: 339.2583 Evaluate side-chains 526 residues out of total 4403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 521 time to evaluate : 3.111 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2551 time to fit residues: 6.7168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 497 random chunks: chunk 313 optimal weight: 20.0000 chunk 420 optimal weight: 0.0060 chunk 120 optimal weight: 0.9980 chunk 363 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 109 optimal weight: 20.0000 chunk 394 optimal weight: 30.0000 chunk 165 optimal weight: 9.9990 chunk 405 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.191738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145522 restraints weight = 56080.641| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 4.69 r_work: 0.3523 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29099 Z= 0.201 Angle : 0.533 10.386 40131 Z= 0.295 Chirality : 0.040 0.221 5362 Planarity : 0.004 0.055 5432 Dihedral : 4.381 24.233 5068 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.57 % Allowed : 38.39 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.12), residues: 4865 helix: 2.50 (0.09), residues: 3500 sheet: -0.36 (0.29), residues: 329 loop : -2.39 (0.17), residues: 1036 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7181.56 seconds wall clock time: 128 minutes 45.90 seconds (7725.90 seconds total)