Starting phenix.real_space_refine on Thu Feb 22 23:59:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2j_22009/02_2024/6x2j_22009_neut_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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: 7 Type Number sf(0) Gaussians Br 4 7.06 5 S 140 5.16 5 C 11692 2.51 5 N 2952 2.21 5 O 3056 1.98 5 F 4 1.80 5 H 18108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 606": "OD1" <-> "OD2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 864": "OE1" <-> "OE2" Residue "A ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 896": "OD1" <-> "OD2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 545": "OD1" <-> "OD2" Residue "B ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 606": "OD1" <-> "OD2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 632": "OE1" <-> "OE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 511": "OD1" <-> "OD2" Residue "C ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 606": "OD1" <-> "OD2" Residue "C GLU 632": "OE1" <-> "OE2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 938": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 981": "OE1" <-> "OE2" Residue "C TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1059": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 592": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 604": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 606": "OD1" <-> "OD2" Residue "D PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 872": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35956 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.17, per 1000 atoms: 0.42 Number of scatterers: 35956 At special positions: 0 Unit cell: (111, 110, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 4 34.99 S 140 16.00 F 4 9.00 O 3056 8.00 N 2952 7.00 C 11692 6.00 H 18108 1.00 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: 33.81 Conformation dependent library (CDL) restraints added in 3.9 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 4 sheets defined 67.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.36 Creating SS restraints... Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 472 through 475 No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 590 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 631 through 641 removed outlier: 3.835A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 713 Processing helix chain 'A' and resid 715 through 738 removed outlier: 4.463A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 767 through 787 Processing helix chain 'A' and resid 804 through 822 removed outlier: 4.061A pdb=" N ILE A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.637A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 891 removed outlier: 4.830A pdb=" N ILE A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.640A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.534A pdb=" N ARG A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 969 removed outlier: 3.503A pdb=" N ASP A 966 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 989 removed outlier: 3.744A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 3.768A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.751A pdb=" N GLN B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.596A pdb=" N GLN B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 527 through 536 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 605 through 608 No H-bonds generated for 'chain 'B' and resid 605 through 608' Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 631 through 641 removed outlier: 3.780A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 713 Processing helix chain 'B' and resid 715 through 738 removed outlier: 4.458A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 767 through 787 Processing helix chain 'B' and resid 804 through 819 removed outlier: 4.132A pdb=" N ILE B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.682A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 891 removed outlier: 4.613A pdb=" N ILE B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 884 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.440A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 928 Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 989 removed outlier: 3.529A pdb=" N ALA B 965 " --> pdb=" O VAL B 961 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 966 " --> pdb=" O GLY B 962 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 3.755A pdb=" N ILE B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU B1045 " --> pdb=" O GLU B1041 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B1063 " --> pdb=" O GLU B1059 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B1064 " --> pdb=" O LYS B1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 Processing helix chain 'C' and resid 459 through 465 removed outlier: 4.433A pdb=" N ARG C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 495 through 503 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 551 through 558 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 593 through 600 Processing helix chain 'C' and resid 605 through 608 No H-bonds generated for 'chain 'C' and resid 605 through 608' Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 631 through 641 removed outlier: 3.783A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 713 Processing helix chain 'C' and resid 715 through 738 removed outlier: 4.465A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 767 through 787 Processing helix chain 'C' and resid 804 through 817 removed outlier: 3.867A pdb=" N TRP C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 828 through 848 removed outlier: 3.529A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 852 No H-bonds generated for 'chain 'C' and resid 850 through 852' Processing helix chain 'C' and resid 854 through 891 removed outlier: 4.465A pdb=" N ILE C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE C 859 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE C 884 " --> pdb=" O LEU C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.380A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 928 Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 968 removed outlier: 3.523A pdb=" N ASP C 966 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 989 removed outlier: 4.361A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 3.909A pdb=" N ILE C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C1045 " --> pdb=" O GLU C1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 459 through 468 removed outlier: 4.278A pdb=" N ARG D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 492 removed outlier: 3.549A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.838A pdb=" N THR D 541 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 622 through 629 Processing helix chain 'D' and resid 631 through 641 removed outlier: 3.763A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 713 Processing helix chain 'D' and resid 715 through 738 removed outlier: 3.623A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 767 through 787 Processing helix chain 'D' and resid 804 through 822 removed outlier: 3.531A pdb=" N TRP D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Proline residue: D 821 - end of helix Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.531A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 891 removed outlier: 4.456A pdb=" N ILE D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE D 859 " --> pdb=" O ASN D 855 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.596A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 928 Processing helix chain 'D' and resid 934 through 947 removed outlier: 3.574A pdb=" N PHE D 938 " --> pdb=" O PRO D 934 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 967 removed outlier: 3.512A pdb=" N ASP D 966 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 989 removed outlier: 4.233A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 3.830A pdb=" N ILE D1044 " --> pdb=" O LEU D1040 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D1045 " --> pdb=" O GLU D1041 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 642 through 644 removed outlier: 4.173A pdb=" N GLU A 657 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 642 through 644 removed outlier: 3.575A pdb=" N GLU B 657 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 656 through 659 Processing sheet with id= D, first strand: chain 'D' and resid 642 through 644 907 hydrogen bonds defined for protein. 2709 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: 14.67 Time building geometry restraints manager: 34.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 7035 1.03 - 1.25: 13477 1.25 - 1.46: 5815 1.46 - 1.68: 9797 1.68 - 1.89: 228 Bond restraints: 36352 Sorted by residual: bond pdb=" N ILE D 803 " pdb=" H ILE D 803 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" N ILE A 803 " pdb=" H ILE A 803 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" N ILE C 803 " pdb=" H ILE C 803 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" N ILE B 803 " pdb=" H ILE B 803 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" CD1 PHE A 841 " pdb=" HD1 PHE A 841 " ideal model delta sigma weight residual 0.930 1.088 -0.158 2.00e-02 2.50e+03 6.21e+01 ... (remaining 36347 not shown) Histogram of bond angle deviations from ideal: 94.51 - 102.68: 217 102.68 - 110.85: 36978 110.85 - 119.02: 14355 119.02 - 127.19: 14035 127.19 - 135.36: 251 Bond angle restraints: 65836 Sorted by residual: angle pdb=" C10 ULJ B1101 " pdb=" C12 ULJ B1101 " pdb=" N16 ULJ B1101 " ideal model delta sigma weight residual 68.56 124.61 -56.05 3.00e+00 1.11e-01 3.49e+02 angle pdb=" C10 ULJ C1101 " pdb=" C12 ULJ C1101 " pdb=" N16 ULJ C1101 " ideal model delta sigma weight residual 68.56 124.57 -56.01 3.00e+00 1.11e-01 3.49e+02 angle pdb=" C10 ULJ A1101 " pdb=" C12 ULJ A1101 " pdb=" N16 ULJ A1101 " ideal model delta sigma weight residual 68.56 124.44 -55.88 3.00e+00 1.11e-01 3.47e+02 angle pdb=" C10 ULJ D1101 " pdb=" C12 ULJ D1101 " pdb=" N16 ULJ D1101 " ideal model delta sigma weight residual 68.56 123.80 -55.24 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C10 ULJ D1101 " pdb=" C12 ULJ D1101 " pdb=" C13 ULJ D1101 " ideal model delta sigma weight residual 176.44 126.32 50.12 3.00e+00 1.11e-01 2.79e+02 ... (remaining 65831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15516 17.99 - 35.98: 912 35.98 - 53.97: 260 53.97 - 71.96: 221 71.96 - 89.95: 63 Dihedral angle restraints: 16972 sinusoidal: 9080 harmonic: 7892 Sorted by residual: dihedral pdb=" CA LYS A 787 " pdb=" C LYS A 787 " pdb=" N GLU A 788 " pdb=" CA GLU A 788 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LYS B 787 " pdb=" C LYS B 787 " pdb=" N GLU B 788 " pdb=" CA GLU B 788 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" C VAL D 948 " pdb=" N VAL D 948 " pdb=" CA VAL D 948 " pdb=" CB VAL D 948 " ideal model delta harmonic sigma weight residual -122.00 -135.43 13.43 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 16969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1638 0.068 - 0.136: 820 0.136 - 0.204: 338 0.204 - 0.272: 72 0.272 - 0.340: 20 Chirality restraints: 2888 Sorted by residual: chirality pdb=" CA PHE C 877 " pdb=" N PHE C 877 " pdb=" C PHE C 877 " pdb=" CB PHE C 877 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 546 " pdb=" N GLU A 546 " pdb=" C GLU A 546 " pdb=" CB GLU A 546 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA VAL D 948 " pdb=" N VAL D 948 " pdb=" C VAL D 948 " pdb=" CB VAL D 948 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2885 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 590 " 0.131 2.00e-02 2.50e+03 4.83e-01 3.51e+03 pdb=" CG ASN C 590 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 590 " -0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN C 590 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 590 " 0.831 2.00e-02 2.50e+03 pdb="HD22 ASN C 590 " -0.824 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 590 " 0.174 2.00e-02 2.50e+03 4.78e-01 3.43e+03 pdb=" CG ASN D 590 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN D 590 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN D 590 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN D 590 " 0.815 2.00e-02 2.50e+03 pdb="HD22 ASN D 590 " -0.805 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 917 " 0.266 2.00e-02 2.50e+03 4.53e-01 3.08e+03 pdb=" CG ASN C 917 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 917 " -0.262 2.00e-02 2.50e+03 pdb=" ND2 ASN C 917 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 917 " -0.729 2.00e-02 2.50e+03 pdb="HD22 ASN C 917 " 0.747 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.25: 2673 2.25 - 2.86: 79363 2.86 - 3.47: 107928 3.47 - 4.09: 142815 4.09 - 4.70: 218954 Nonbonded interactions: 551733 Sorted by model distance: nonbonded pdb=" OE1 GLU D 808 " pdb=" HH TYR D 812 " model vdw 1.635 1.850 nonbonded pdb=" OE1 GLU B 808 " pdb=" HH TYR B 812 " model vdw 1.645 1.850 nonbonded pdb=" OE1 GLU C 808 " pdb=" HH TYR C 812 " model vdw 1.650 1.850 nonbonded pdb=" HG SER A1039 " pdb=" OE1 GLU A1043 " model vdw 1.651 1.850 nonbonded pdb=" HG SER C1076 " pdb=" OE2 GLU C1077 " model vdw 1.651 1.850 ... (remaining 551728 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' } 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: 1.670 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: 0.510 Extract box with map and model: 8.760 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 120.200 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.180 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 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 : 0.014 0.139 18244 Z= 0.932 Angle : 2.116 56.052 24712 Z= 1.323 Chirality : 0.093 0.340 2888 Planarity : 0.014 0.174 3020 Dihedral : 13.749 88.454 6568 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.70 % Favored : 95.98 % Rotamer: Outliers : 1.34 % Allowed : 5.37 % Favored : 93.29 % Cbeta Deviations : 0.19 % 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: -2.17 (0.16), residues: 2188 helix: -1.67 (0.10), residues: 1648 sheet: 3.69 (0.79), residues: 20 loop : -0.02 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.014 TRP B 711 HIS 0.018 0.002 HIS C 519 PHE 0.047 0.008 PHE D 746 TYR 0.174 0.020 TYR D 785 ARG 0.016 0.002 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 741 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 715 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 LYS cc_start: 0.7225 (mttt) cc_final: 0.7008 (mmmt) REVERT: A 523 MET cc_start: 0.7714 (tpt) cc_final: 0.7423 (tpt) REVERT: A 528 GLN cc_start: 0.6952 (mm-40) cc_final: 0.6143 (mm-40) REVERT: A 544 LEU cc_start: 0.8326 (mt) cc_final: 0.7955 (mm) REVERT: A 547 ASP cc_start: 0.7390 (t0) cc_final: 0.6909 (t0) REVERT: A 558 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6308 (mp0) REVERT: A 562 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7117 (mtmm) REVERT: A 575 VAL cc_start: 0.7905 (p) cc_final: 0.7705 (m) REVERT: A 589 HIS cc_start: 0.7630 (m170) cc_final: 0.7337 (m-70) REVERT: A 590 ASN cc_start: 0.7451 (m-40) cc_final: 0.7119 (m110) REVERT: A 594 GLU cc_start: 0.7168 (tp30) cc_final: 0.6964 (tp30) REVERT: A 597 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6358 (mt) REVERT: A 603 LYS cc_start: 0.8138 (mttt) cc_final: 0.7846 (tttm) REVERT: A 606 ASP cc_start: 0.7724 (m-30) cc_final: 0.7447 (m-30) REVERT: A 607 GLU cc_start: 0.6398 (tt0) cc_final: 0.6036 (tt0) REVERT: A 628 GLU cc_start: 0.7154 (tt0) cc_final: 0.6348 (tm-30) REVERT: A 634 MET cc_start: 0.7431 (tpt) cc_final: 0.6983 (tpt) REVERT: A 640 PHE cc_start: 0.6765 (m-80) cc_final: 0.6085 (m-10) REVERT: A 642 MET cc_start: 0.6864 (mtp) cc_final: 0.6462 (mtm) REVERT: A 716 PHE cc_start: 0.7496 (t80) cc_final: 0.7231 (t80) REVERT: A 717 ARG cc_start: 0.6742 (ttt180) cc_final: 0.5690 (ttp80) REVERT: A 720 MET cc_start: 0.6817 (mmm) cc_final: 0.6025 (mpm) REVERT: A 721 MET cc_start: 0.6499 (ttm) cc_final: 0.6191 (tpt) REVERT: A 727 CYS cc_start: 0.7666 (t) cc_final: 0.6830 (m) REVERT: A 731 ILE cc_start: 0.7477 (mt) cc_final: 0.7158 (mm) REVERT: A 744 MET cc_start: 0.7052 (mmt) cc_final: 0.6835 (mmm) REVERT: A 845 ASN cc_start: 0.8824 (t0) cc_final: 0.8534 (t0) REVERT: A 864 GLU cc_start: 0.6283 (tt0) cc_final: 0.5337 (tm-30) REVERT: A 868 LYS cc_start: 0.6919 (mttm) cc_final: 0.6324 (mtpm) REVERT: A 875 VAL cc_start: 0.8204 (t) cc_final: 0.7965 (p) REVERT: A 877 PHE cc_start: 0.7074 (m-10) cc_final: 0.6676 (m-80) REVERT: A 882 LEU cc_start: 0.8272 (tp) cc_final: 0.8070 (tp) REVERT: A 930 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6546 (mt-10) REVERT: A 981 GLU cc_start: 0.7727 (tp30) cc_final: 0.7388 (tt0) REVERT: A 993 TRP cc_start: 0.7409 (p-90) cc_final: 0.7196 (p-90) REVERT: A 1001 LYS cc_start: 0.6894 (mmtp) cc_final: 0.6585 (mtmm) REVERT: A 1050 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6623 (ttm-80) REVERT: B 503 LYS cc_start: 0.6536 (tttt) cc_final: 0.6242 (tppp) REVERT: B 528 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6471 (mm-40) REVERT: B 544 LEU cc_start: 0.7444 (mt) cc_final: 0.6969 (mm) REVERT: B 558 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6714 (mp0) REVERT: B 575 VAL cc_start: 0.8640 (p) cc_final: 0.8326 (m) REVERT: B 594 GLU cc_start: 0.6832 (tp30) cc_final: 0.6577 (mm-30) REVERT: B 607 GLU cc_start: 0.6367 (tt0) cc_final: 0.5972 (tt0) REVERT: B 628 GLU cc_start: 0.7245 (tt0) cc_final: 0.6643 (tm-30) REVERT: B 629 TYR cc_start: 0.7732 (m-80) cc_final: 0.7337 (m-80) REVERT: B 634 MET cc_start: 0.7324 (tpt) cc_final: 0.7084 (tpt) REVERT: B 640 PHE cc_start: 0.7022 (m-80) cc_final: 0.6472 (m-10) REVERT: B 642 MET cc_start: 0.7062 (mtp) cc_final: 0.6596 (mtm) REVERT: B 687 ASN cc_start: 0.7481 (m-40) cc_final: 0.6823 (m-40) REVERT: B 689 MET cc_start: 0.7879 (mtt) cc_final: 0.7522 (mtm) REVERT: B 693 ASN cc_start: 0.7569 (m-40) cc_final: 0.7356 (t0) REVERT: B 695 ILE cc_start: 0.7228 (tt) cc_final: 0.6519 (tp) REVERT: B 699 ASN cc_start: 0.7297 (m-40) cc_final: 0.6599 (m110) REVERT: B 704 LYS cc_start: 0.6563 (mttt) cc_final: 0.5685 (mmtm) REVERT: B 717 ARG cc_start: 0.6681 (ttt180) cc_final: 0.5857 (mtp85) REVERT: B 720 MET cc_start: 0.6715 (mmm) cc_final: 0.6483 (mmp) REVERT: B 721 MET cc_start: 0.6447 (ttm) cc_final: 0.6108 (tpt) REVERT: B 727 CYS cc_start: 0.7974 (t) cc_final: 0.6842 (m) REVERT: B 845 ASN cc_start: 0.8747 (t0) cc_final: 0.8345 (t0) REVERT: B 864 GLU cc_start: 0.6499 (tt0) cc_final: 0.5697 (mm-30) REVERT: B 868 LYS cc_start: 0.6759 (mttm) cc_final: 0.6227 (mtpm) REVERT: B 882 LEU cc_start: 0.8099 (tp) cc_final: 0.7834 (tp) REVERT: B 896 ASP cc_start: 0.7734 (m-30) cc_final: 0.7455 (m-30) REVERT: B 930 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6790 (mt-10) REVERT: B 966 ASP cc_start: 0.5289 (m-30) cc_final: 0.4962 (m-30) REVERT: B 972 SER cc_start: 0.7941 (t) cc_final: 0.7425 (p) REVERT: B 1001 LYS cc_start: 0.7463 (mmtp) cc_final: 0.6821 (mtmm) REVERT: B 1052 LYS cc_start: 0.6731 (ttmt) cc_final: 0.6359 (tttp) REVERT: B 1063 GLU cc_start: 0.7627 (tp30) cc_final: 0.7013 (mm-30) REVERT: B 1070 GLN cc_start: 0.7665 (tt0) cc_final: 0.7458 (tt0) REVERT: C 460 ASN cc_start: 0.7273 (t0) cc_final: 0.6995 (t0) REVERT: C 467 GLN cc_start: 0.7496 (tt0) cc_final: 0.7130 (mm-40) REVERT: C 496 LYS cc_start: 0.7384 (mttt) cc_final: 0.7073 (mptp) REVERT: C 558 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7166 (mp0) REVERT: C 626 MET cc_start: 0.7464 (mtp) cc_final: 0.7205 (ttm) REVERT: C 628 GLU cc_start: 0.7116 (tt0) cc_final: 0.6439 (tt0) REVERT: C 629 TYR cc_start: 0.7639 (m-80) cc_final: 0.7225 (m-80) REVERT: C 635 LYS cc_start: 0.6359 (ttpt) cc_final: 0.5775 (tptp) REVERT: C 640 PHE cc_start: 0.6659 (m-80) cc_final: 0.6211 (m-10) REVERT: C 687 ASN cc_start: 0.7772 (m-40) cc_final: 0.7182 (m110) REVERT: C 691 GLN cc_start: 0.7499 (mt0) cc_final: 0.7040 (mm-40) REVERT: C 695 ILE cc_start: 0.7224 (tt) cc_final: 0.6970 (tp) REVERT: C 699 ASN cc_start: 0.7130 (m-40) cc_final: 0.6711 (m110) REVERT: C 705 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6517 (mm-30) REVERT: C 721 MET cc_start: 0.6444 (ttm) cc_final: 0.5856 (tpp) REVERT: C 727 CYS cc_start: 0.7684 (t) cc_final: 0.6816 (m) REVERT: C 731 ILE cc_start: 0.7766 (mt) cc_final: 0.7526 (mm) REVERT: C 735 ILE cc_start: 0.8101 (mt) cc_final: 0.7885 (mm) REVERT: C 751 ILE cc_start: 0.6233 (mt) cc_final: 0.5973 (mt) REVERT: C 819 VAL cc_start: 0.8815 (t) cc_final: 0.8615 (m) REVERT: C 833 GLN cc_start: 0.7235 (tt0) cc_final: 0.6964 (tm-30) REVERT: C 842 TYR cc_start: 0.7965 (m-80) cc_final: 0.7715 (m-80) REVERT: C 845 ASN cc_start: 0.8669 (t0) cc_final: 0.8444 (t0) REVERT: C 864 GLU cc_start: 0.6678 (tt0) cc_final: 0.5794 (mm-30) REVERT: C 868 LYS cc_start: 0.6653 (mttm) cc_final: 0.5948 (mtmm) REVERT: C 896 ASP cc_start: 0.7928 (m-30) cc_final: 0.7698 (m-30) REVERT: C 930 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6900 (mt-10) REVERT: C 972 SER cc_start: 0.7691 (t) cc_final: 0.7182 (p) REVERT: C 978 MET cc_start: 0.7906 (mtm) cc_final: 0.7669 (mtp) REVERT: C 981 GLU cc_start: 0.7678 (tp30) cc_final: 0.7327 (tt0) REVERT: C 1001 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6713 (mtmm) REVERT: C 1048 LYS cc_start: 0.6145 (ttmm) cc_final: 0.5851 (ttpp) REVERT: C 1049 TYR cc_start: 0.7221 (m-80) cc_final: 0.6808 (m-80) REVERT: C 1052 LYS cc_start: 0.6719 (ttmt) cc_final: 0.6295 (tttp) REVERT: D 504 LYS cc_start: 0.6514 (mmtm) cc_final: 0.6195 (mtpp) REVERT: D 558 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6674 (mp0) REVERT: D 562 LYS cc_start: 0.7608 (mttt) cc_final: 0.7233 (mtpm) REVERT: D 575 VAL cc_start: 0.8607 (p) cc_final: 0.8286 (m) REVERT: D 593 LYS cc_start: 0.7069 (ttpt) cc_final: 0.6798 (tttm) REVERT: D 594 GLU cc_start: 0.6943 (tp30) cc_final: 0.6523 (mm-30) REVERT: D 603 LYS cc_start: 0.8244 (mttt) cc_final: 0.7992 (tttm) REVERT: D 607 GLU cc_start: 0.6342 (tt0) cc_final: 0.5918 (tt0) REVERT: D 628 GLU cc_start: 0.7109 (tt0) cc_final: 0.6377 (tt0) REVERT: D 640 PHE cc_start: 0.6258 (m-80) cc_final: 0.5780 (m-10) REVERT: D 664 GLN cc_start: 0.7923 (pt0) cc_final: 0.7397 (mt0) REVERT: D 693 ASN cc_start: 0.7248 (m-40) cc_final: 0.7002 (t0) REVERT: D 704 LYS cc_start: 0.6332 (mttt) cc_final: 0.5186 (mmpt) REVERT: D 705 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6269 (mm-30) REVERT: D 717 ARG cc_start: 0.6569 (ttt180) cc_final: 0.5769 (ttp80) REVERT: D 720 MET cc_start: 0.6589 (mmm) cc_final: 0.6050 (mmp) REVERT: D 868 LYS cc_start: 0.6644 (mttm) cc_final: 0.6126 (mtpm) REVERT: D 882 LEU cc_start: 0.8087 (tp) cc_final: 0.7867 (tp) REVERT: D 966 ASP cc_start: 0.4986 (m-30) cc_final: 0.4773 (m-30) REVERT: D 972 SER cc_start: 0.7630 (t) cc_final: 0.7136 (p) REVERT: D 989 LYS cc_start: 0.6879 (mtmt) cc_final: 0.6656 (mtpm) REVERT: D 1001 LYS cc_start: 0.6615 (mmtp) cc_final: 0.6245 (mppt) REVERT: D 1050 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.6337 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6973 (ttmt) cc_final: 0.6632 (tttm) outliers start: 26 outliers final: 8 residues processed: 724 average time/residue: 2.0509 time to fit residues: 1726.7083 Evaluate side-chains 539 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 530 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 PRO Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 449 PRO Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 485 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A 494 HIS A1070 GLN B 463 GLN B 487 HIS B 492 ASN B 829 HIS C 831 GLN C 851 GLN C1061 GLN D 590 ASN D 829 HIS D1061 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18244 Z= 0.223 Angle : 0.602 7.241 24712 Z= 0.311 Chirality : 0.039 0.179 2888 Planarity : 0.004 0.062 3020 Dihedral : 6.611 86.394 2395 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 14.57 % Favored : 83.21 % 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: -0.19 (0.17), residues: 2188 helix: -0.10 (0.12), residues: 1644 sheet: 0.41 (0.64), residues: 40 loop : 0.34 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 832 HIS 0.006 0.001 HIS C 451 PHE 0.017 0.001 PHE A 818 TYR 0.017 0.002 TYR C 840 ARG 0.003 0.000 ARG C1050 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 580 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 537 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 LYS cc_start: 0.7105 (mttt) cc_final: 0.6840 (mmtm) REVERT: A 523 MET cc_start: 0.7672 (tpt) cc_final: 0.7445 (tpt) REVERT: A 547 ASP cc_start: 0.7572 (t0) cc_final: 0.7006 (t0) REVERT: A 562 LYS cc_start: 0.7332 (mmtt) cc_final: 0.7099 (ttmm) REVERT: A 591 LYS cc_start: 0.7807 (mttt) cc_final: 0.7329 (mttm) REVERT: A 594 GLU cc_start: 0.7404 (tp30) cc_final: 0.7172 (tp30) REVERT: A 597 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6366 (mt) REVERT: A 603 LYS cc_start: 0.8245 (mttt) cc_final: 0.8039 (tttt) REVERT: A 606 ASP cc_start: 0.7792 (m-30) cc_final: 0.6584 (p0) REVERT: A 607 GLU cc_start: 0.6158 (tt0) cc_final: 0.5880 (tt0) REVERT: A 628 GLU cc_start: 0.7342 (tt0) cc_final: 0.6741 (tm-30) REVERT: A 634 MET cc_start: 0.7189 (tpt) cc_final: 0.6751 (tpt) REVERT: A 640 PHE cc_start: 0.6208 (m-80) cc_final: 0.5541 (m-10) REVERT: A 699 ASN cc_start: 0.7177 (m-40) cc_final: 0.6599 (m110) REVERT: A 704 LYS cc_start: 0.6310 (mttt) cc_final: 0.5299 (mmpt) REVERT: A 716 PHE cc_start: 0.7240 (t80) cc_final: 0.7011 (t80) REVERT: A 720 MET cc_start: 0.6423 (mmm) cc_final: 0.5885 (mmp) REVERT: A 721 MET cc_start: 0.6013 (ttm) cc_final: 0.5574 (tpt) REVERT: A 727 CYS cc_start: 0.7486 (t) cc_final: 0.6959 (m) REVERT: A 744 MET cc_start: 0.6926 (mmt) cc_final: 0.6642 (mmm) REVERT: A 808 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6223 (mt-10) REVERT: A 845 ASN cc_start: 0.8513 (t0) cc_final: 0.7874 (t0) REVERT: A 852 ARG cc_start: 0.6504 (mmt90) cc_final: 0.6182 (mmt-90) REVERT: A 864 GLU cc_start: 0.6261 (tt0) cc_final: 0.5674 (mm-30) REVERT: A 868 LYS cc_start: 0.6468 (mttm) cc_final: 0.5933 (mtpm) REVERT: A 877 PHE cc_start: 0.6407 (m-10) cc_final: 0.5727 (m-80) REVERT: A 882 LEU cc_start: 0.7665 (tp) cc_final: 0.7404 (tp) REVERT: A 928 ARG cc_start: 0.7320 (mtm-85) cc_final: 0.7093 (mtm-85) REVERT: A 930 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6367 (mm-30) REVERT: A 986 LEU cc_start: 0.7127 (mm) cc_final: 0.6766 (mp) REVERT: A 995 LEU cc_start: 0.7619 (mm) cc_final: 0.7400 (mm) REVERT: A 1001 LYS cc_start: 0.6810 (mmtp) cc_final: 0.6516 (mtmm) REVERT: B 528 GLN cc_start: 0.6925 (mm-40) cc_final: 0.6538 (mm-40) REVERT: B 544 LEU cc_start: 0.7234 (mt) cc_final: 0.6794 (mm) REVERT: B 575 VAL cc_start: 0.8232 (p) cc_final: 0.7803 (m) REVERT: B 593 LYS cc_start: 0.7343 (ttpt) cc_final: 0.7002 (tttm) REVERT: B 594 GLU cc_start: 0.6908 (tp30) cc_final: 0.6372 (mm-30) REVERT: B 607 GLU cc_start: 0.6301 (tt0) cc_final: 0.5987 (tt0) REVERT: B 628 GLU cc_start: 0.7357 (tt0) cc_final: 0.6557 (tm-30) REVERT: B 629 TYR cc_start: 0.7720 (m-80) cc_final: 0.7245 (m-80) REVERT: B 634 MET cc_start: 0.7190 (tpt) cc_final: 0.6915 (tpt) REVERT: B 640 PHE cc_start: 0.6218 (m-80) cc_final: 0.5403 (m-80) REVERT: B 642 MET cc_start: 0.6825 (mtp) cc_final: 0.6523 (mtm) REVERT: B 687 ASN cc_start: 0.7495 (m-40) cc_final: 0.6738 (m110) REVERT: B 695 ILE cc_start: 0.7302 (tt) cc_final: 0.6836 (tp) REVERT: B 698 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6186 (mt) REVERT: B 699 ASN cc_start: 0.7230 (m-40) cc_final: 0.6687 (m-40) REVERT: B 704 LYS cc_start: 0.6405 (mttt) cc_final: 0.5572 (mmtp) REVERT: B 721 MET cc_start: 0.6270 (ttm) cc_final: 0.5965 (tpt) REVERT: B 727 CYS cc_start: 0.7616 (t) cc_final: 0.6884 (m) REVERT: B 731 ILE cc_start: 0.7432 (mt) cc_final: 0.7187 (mm) REVERT: B 851 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6600 (mt0) REVERT: B 864 GLU cc_start: 0.6644 (tt0) cc_final: 0.5854 (mm-30) REVERT: B 868 LYS cc_start: 0.6556 (mttm) cc_final: 0.6046 (mtpm) REVERT: B 896 ASP cc_start: 0.7746 (m-30) cc_final: 0.7452 (m-30) REVERT: B 928 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6866 (mtm-85) REVERT: B 966 ASP cc_start: 0.5070 (m-30) cc_final: 0.4805 (m-30) REVERT: B 972 SER cc_start: 0.7722 (t) cc_final: 0.7328 (p) REVERT: B 1001 LYS cc_start: 0.7153 (mmtp) cc_final: 0.6771 (mtmm) REVERT: B 1052 LYS cc_start: 0.6587 (ttmt) cc_final: 0.6234 (ptmm) REVERT: B 1063 GLU cc_start: 0.7154 (tp30) cc_final: 0.6763 (mm-30) REVERT: C 496 LYS cc_start: 0.7228 (mttt) cc_final: 0.6991 (mptm) REVERT: C 504 LYS cc_start: 0.6693 (mmtm) cc_final: 0.6465 (mtpp) REVERT: C 530 MET cc_start: 0.8036 (mtm) cc_final: 0.7661 (mtm) REVERT: C 571 ASN cc_start: 0.8097 (m110) cc_final: 0.7414 (t0) REVERT: C 575 VAL cc_start: 0.7809 (p) cc_final: 0.7535 (m) REVERT: C 628 GLU cc_start: 0.7079 (tt0) cc_final: 0.6494 (tt0) REVERT: C 642 MET cc_start: 0.6667 (mtm) cc_final: 0.6453 (mtm) REVERT: C 643 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7163 (mm) REVERT: C 691 GLN cc_start: 0.7595 (mt0) cc_final: 0.7026 (mm-40) REVERT: C 699 ASN cc_start: 0.7202 (m-40) cc_final: 0.6774 (m110) REVERT: C 704 LYS cc_start: 0.6272 (mttt) cc_final: 0.5773 (mttp) REVERT: C 720 MET cc_start: 0.6396 (mmm) cc_final: 0.5813 (mmp) REVERT: C 721 MET cc_start: 0.6234 (ttm) cc_final: 0.5661 (tpp) REVERT: C 727 CYS cc_start: 0.7255 (t) cc_final: 0.6630 (m) REVERT: C 731 ILE cc_start: 0.7846 (mt) cc_final: 0.7600 (mm) REVERT: C 735 ILE cc_start: 0.8023 (mt) cc_final: 0.7795 (mm) REVERT: C 808 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6417 (mt-10) REVERT: C 833 GLN cc_start: 0.6617 (tt0) cc_final: 0.6321 (tt0) REVERT: C 845 ASN cc_start: 0.8386 (t0) cc_final: 0.7875 (t0) REVERT: C 854 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6577 (mt-10) REVERT: C 864 GLU cc_start: 0.6517 (tt0) cc_final: 0.5731 (mm-30) REVERT: C 868 LYS cc_start: 0.6298 (mttm) cc_final: 0.5711 (mtmp) REVERT: C 896 ASP cc_start: 0.7808 (m-30) cc_final: 0.7589 (m-30) REVERT: C 911 MET cc_start: 0.8147 (mtm) cc_final: 0.7853 (mtm) REVERT: C 920 GLU cc_start: 0.6994 (tt0) cc_final: 0.6611 (tt0) REVERT: C 928 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7108 (mtm-85) REVERT: C 930 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6878 (mt-10) REVERT: C 972 SER cc_start: 0.7755 (t) cc_final: 0.7303 (p) REVERT: C 981 GLU cc_start: 0.7457 (tp30) cc_final: 0.7167 (tt0) REVERT: C 987 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6615 (mm-30) REVERT: C 1001 LYS cc_start: 0.7136 (mmtp) cc_final: 0.6752 (mtmm) REVERT: C 1052 LYS cc_start: 0.6509 (ttmt) cc_final: 0.6171 (ttpp) REVERT: D 504 LYS cc_start: 0.6416 (mmtm) cc_final: 0.6069 (mtpp) REVERT: D 558 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6567 (mm-30) REVERT: D 562 LYS cc_start: 0.7294 (mttt) cc_final: 0.6990 (ttmm) REVERT: D 575 VAL cc_start: 0.8291 (p) cc_final: 0.7881 (m) REVERT: D 591 LYS cc_start: 0.7707 (mttt) cc_final: 0.7368 (mttp) REVERT: D 593 LYS cc_start: 0.7377 (ttpt) cc_final: 0.7038 (tttm) REVERT: D 603 LYS cc_start: 0.8284 (mttt) cc_final: 0.8059 (tttm) REVERT: D 607 GLU cc_start: 0.6200 (tt0) cc_final: 0.5738 (tt0) REVERT: D 626 MET cc_start: 0.7054 (mtp) cc_final: 0.6765 (ttm) REVERT: D 628 GLU cc_start: 0.7072 (tt0) cc_final: 0.6122 (tm-30) REVERT: D 693 ASN cc_start: 0.7291 (m-40) cc_final: 0.7032 (t0) REVERT: D 699 ASN cc_start: 0.7093 (m-40) cc_final: 0.6430 (m-40) REVERT: D 704 LYS cc_start: 0.6151 (mttt) cc_final: 0.5001 (mmpt) REVERT: D 705 GLU cc_start: 0.6374 (mm-30) cc_final: 0.6032 (mm-30) REVERT: D 717 ARG cc_start: 0.6251 (ttt180) cc_final: 0.5934 (ttp-170) REVERT: D 720 MET cc_start: 0.6384 (mmm) cc_final: 0.5703 (mmp) REVERT: D 727 CYS cc_start: 0.7171 (t) cc_final: 0.6803 (m) REVERT: D 852 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.6124 (mmt90) REVERT: D 864 GLU cc_start: 0.5480 (tp30) cc_final: 0.5202 (tp30) REVERT: D 868 LYS cc_start: 0.6558 (mttm) cc_final: 0.6038 (mtpm) REVERT: D 928 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7126 (mtm-85) REVERT: D 966 ASP cc_start: 0.5042 (m-30) cc_final: 0.4782 (m-30) REVERT: D 972 SER cc_start: 0.7397 (t) cc_final: 0.7086 (p) REVERT: D 981 GLU cc_start: 0.7336 (tp30) cc_final: 0.6972 (tt0) REVERT: D 983 HIS cc_start: 0.7795 (m-70) cc_final: 0.7534 (m-70) REVERT: D 1001 LYS cc_start: 0.6675 (mmtp) cc_final: 0.6380 (mtmm) REVERT: D 1050 ARG cc_start: 0.6568 (ttm-80) cc_final: 0.6246 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6754 (ttmt) cc_final: 0.6506 (tttm) outliers start: 43 outliers final: 13 residues processed: 561 average time/residue: 2.1474 time to fit residues: 1394.3924 Evaluate side-chains 489 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 470 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 851 GLN Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 987 GLU Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 900 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 460 ASN B 644 HIS B 700 HIS B1070 GLN C 460 ASN C 494 HIS ** C 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 GLN C 893 ASN C 907 GLN D 460 ASN D 687 ASN ** D 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 829 HIS D 851 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18244 Z= 0.315 Angle : 0.596 6.118 24712 Z= 0.306 Chirality : 0.040 0.212 2888 Planarity : 0.004 0.062 3020 Dihedral : 5.672 58.415 2381 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 2.63 % Allowed : 17.46 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2188 helix: 0.45 (0.12), residues: 1648 sheet: -1.34 (0.65), residues: 48 loop : 0.19 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 711 HIS 0.008 0.002 HIS C 451 PHE 0.013 0.002 PHE C 877 TYR 0.026 0.002 TYR C 842 ARG 0.004 0.001 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 528 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 477 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 LYS cc_start: 0.7078 (mttt) cc_final: 0.6787 (mmtm) REVERT: A 544 LEU cc_start: 0.8107 (mt) cc_final: 0.7630 (mm) REVERT: A 547 ASP cc_start: 0.7384 (t0) cc_final: 0.6694 (t0) REVERT: A 562 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7135 (ttmm) REVERT: A 591 LYS cc_start: 0.7780 (mttt) cc_final: 0.7336 (mttm) REVERT: A 597 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6397 (mt) REVERT: A 603 LYS cc_start: 0.8298 (mttt) cc_final: 0.8068 (tttm) REVERT: A 606 ASP cc_start: 0.7728 (m-30) cc_final: 0.6721 (p0) REVERT: A 634 MET cc_start: 0.7262 (tpt) cc_final: 0.6820 (tpt) REVERT: A 640 PHE cc_start: 0.6333 (m-80) cc_final: 0.5517 (m-10) REVERT: A 642 MET cc_start: 0.6491 (mtm) cc_final: 0.6233 (mtm) REVERT: A 664 GLN cc_start: 0.7634 (pt0) cc_final: 0.7297 (tp40) REVERT: A 699 ASN cc_start: 0.7190 (m-40) cc_final: 0.6636 (m110) REVERT: A 704 LYS cc_start: 0.6214 (mttt) cc_final: 0.5439 (mmtp) REVERT: A 720 MET cc_start: 0.6376 (mmm) cc_final: 0.5857 (mmp) REVERT: A 721 MET cc_start: 0.5919 (ttm) cc_final: 0.5528 (tpt) REVERT: A 727 CYS cc_start: 0.7085 (t) cc_final: 0.6607 (m) REVERT: A 744 MET cc_start: 0.6888 (mmt) cc_final: 0.6614 (mmm) REVERT: A 808 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6162 (mt-10) REVERT: A 852 ARG cc_start: 0.6438 (mmt90) cc_final: 0.6046 (mmt-90) REVERT: A 864 GLU cc_start: 0.6460 (tt0) cc_final: 0.5685 (mm-30) REVERT: A 868 LYS cc_start: 0.6254 (mttm) cc_final: 0.5803 (mtpm) REVERT: A 877 PHE cc_start: 0.6506 (m-10) cc_final: 0.5812 (m-80) REVERT: A 882 LEU cc_start: 0.7652 (tp) cc_final: 0.7396 (tp) REVERT: A 912 MET cc_start: 0.7380 (ttp) cc_final: 0.7047 (ttm) REVERT: A 928 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7275 (mtm-85) REVERT: A 930 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6152 (mm-30) REVERT: A 986 LEU cc_start: 0.7176 (mm) cc_final: 0.6803 (mp) REVERT: A 1001 LYS cc_start: 0.6919 (mmtp) cc_final: 0.6448 (mtmm) REVERT: B 528 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6616 (mm110) REVERT: B 544 LEU cc_start: 0.7299 (mt) cc_final: 0.6829 (mm) REVERT: B 546 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6100 (pp20) REVERT: B 575 VAL cc_start: 0.8461 (p) cc_final: 0.8072 (m) REVERT: B 593 LYS cc_start: 0.7441 (ttpt) cc_final: 0.7010 (tttm) REVERT: B 607 GLU cc_start: 0.6226 (tt0) cc_final: 0.5837 (tt0) REVERT: B 628 GLU cc_start: 0.7333 (tt0) cc_final: 0.6377 (tm-30) REVERT: B 629 TYR cc_start: 0.7664 (m-80) cc_final: 0.7279 (m-80) REVERT: B 634 MET cc_start: 0.7356 (tpt) cc_final: 0.7097 (tpt) REVERT: B 640 PHE cc_start: 0.6287 (m-80) cc_final: 0.5720 (m-10) REVERT: B 642 MET cc_start: 0.6740 (mtp) cc_final: 0.6438 (mtp) REVERT: B 687 ASN cc_start: 0.7450 (m-40) cc_final: 0.6673 (m110) REVERT: B 695 ILE cc_start: 0.7129 (tt) cc_final: 0.6538 (tp) REVERT: B 698 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6280 (mt) REVERT: B 699 ASN cc_start: 0.7156 (m-40) cc_final: 0.6530 (m110) REVERT: B 704 LYS cc_start: 0.6427 (mttt) cc_final: 0.5683 (mmtp) REVERT: B 721 MET cc_start: 0.6211 (ttm) cc_final: 0.5771 (tpt) REVERT: B 727 CYS cc_start: 0.7554 (t) cc_final: 0.6989 (m) REVERT: B 731 ILE cc_start: 0.7587 (mt) cc_final: 0.7367 (mm) REVERT: B 808 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5960 (mt-10) REVERT: B 864 GLU cc_start: 0.6594 (tt0) cc_final: 0.5737 (mm-30) REVERT: B 868 LYS cc_start: 0.6517 (mttm) cc_final: 0.6034 (mtpm) REVERT: B 873 SER cc_start: 0.6504 (t) cc_final: 0.6290 (p) REVERT: B 896 ASP cc_start: 0.7846 (m-30) cc_final: 0.7546 (m-30) REVERT: B 909 PHE cc_start: 0.7522 (t80) cc_final: 0.7183 (t80) REVERT: B 928 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6860 (mtm-85) REVERT: B 966 ASP cc_start: 0.5392 (m-30) cc_final: 0.5013 (m-30) REVERT: B 972 SER cc_start: 0.7532 (t) cc_final: 0.7132 (p) REVERT: B 981 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6459 (mm-30) REVERT: B 1001 LYS cc_start: 0.7146 (mmtp) cc_final: 0.6767 (mtmm) REVERT: B 1042 MET cc_start: 0.6425 (pp-130) cc_final: 0.6190 (pp-130) REVERT: B 1052 LYS cc_start: 0.6486 (ttmt) cc_final: 0.6110 (ptmt) REVERT: B 1063 GLU cc_start: 0.7154 (tp30) cc_final: 0.6732 (mm-30) REVERT: C 481 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6514 (m-70) REVERT: C 496 LYS cc_start: 0.7050 (mttt) cc_final: 0.6776 (mptm) REVERT: C 504 LYS cc_start: 0.6811 (mmtm) cc_final: 0.6558 (mtpp) REVERT: C 571 ASN cc_start: 0.8258 (m110) cc_final: 0.7575 (t0) REVERT: C 606 ASP cc_start: 0.7581 (m-30) cc_final: 0.6482 (p0) REVERT: C 628 GLU cc_start: 0.7118 (tt0) cc_final: 0.6543 (tt0) REVERT: C 640 PHE cc_start: 0.6248 (m-80) cc_final: 0.5657 (m-10) REVERT: C 687 ASN cc_start: 0.7458 (m-40) cc_final: 0.7125 (m110) REVERT: C 689 MET cc_start: 0.7789 (mtt) cc_final: 0.7490 (mtt) REVERT: C 691 GLN cc_start: 0.7534 (mt0) cc_final: 0.6992 (mm-40) REVERT: C 699 ASN cc_start: 0.7154 (m-40) cc_final: 0.6897 (m110) REVERT: C 720 MET cc_start: 0.6292 (mmm) cc_final: 0.5761 (mmp) REVERT: C 721 MET cc_start: 0.6185 (ttm) cc_final: 0.5696 (tpp) REVERT: C 727 CYS cc_start: 0.7371 (t) cc_final: 0.6794 (m) REVERT: C 731 ILE cc_start: 0.8008 (mt) cc_final: 0.7761 (mm) REVERT: C 808 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6264 (mt-10) REVERT: C 854 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6620 (mt-10) REVERT: C 864 GLU cc_start: 0.6341 (tt0) cc_final: 0.5597 (tp30) REVERT: C 868 LYS cc_start: 0.6379 (mttm) cc_final: 0.5832 (mtmp) REVERT: C 896 ASP cc_start: 0.7884 (m-30) cc_final: 0.7672 (m-30) REVERT: C 972 SER cc_start: 0.7683 (t) cc_final: 0.7319 (p) REVERT: C 986 LEU cc_start: 0.7667 (mm) cc_final: 0.7365 (mp) REVERT: C 987 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6803 (mm-30) REVERT: C 1001 LYS cc_start: 0.7146 (mmtp) cc_final: 0.6762 (mtmm) REVERT: C 1059 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6076 (mm-30) REVERT: D 504 LYS cc_start: 0.6531 (mmtm) cc_final: 0.6291 (mtpp) REVERT: D 528 GLN cc_start: 0.6508 (mm-40) cc_final: 0.5826 (mm-40) REVERT: D 544 LEU cc_start: 0.7720 (mt) cc_final: 0.7136 (mm) REVERT: D 562 LYS cc_start: 0.6927 (mttt) cc_final: 0.6651 (ttmm) REVERT: D 575 VAL cc_start: 0.8455 (p) cc_final: 0.8060 (m) REVERT: D 593 LYS cc_start: 0.7408 (ttpt) cc_final: 0.7072 (tttm) REVERT: D 603 LYS cc_start: 0.8280 (mttt) cc_final: 0.7956 (tmmt) REVERT: D 606 ASP cc_start: 0.7665 (m-30) cc_final: 0.6306 (p0) REVERT: D 628 GLU cc_start: 0.7016 (tt0) cc_final: 0.6131 (tm-30) REVERT: D 640 PHE cc_start: 0.6163 (m-80) cc_final: 0.5635 (m-10) REVERT: D 699 ASN cc_start: 0.7127 (m-40) cc_final: 0.6255 (m-40) REVERT: D 704 LYS cc_start: 0.5909 (mttt) cc_final: 0.4890 (mmpt) REVERT: D 717 ARG cc_start: 0.6241 (ttt180) cc_final: 0.5911 (ttp-170) REVERT: D 720 MET cc_start: 0.6404 (mmm) cc_final: 0.5698 (mmp) REVERT: D 727 CYS cc_start: 0.7263 (t) cc_final: 0.7015 (m) REVERT: D 852 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6217 (mmt90) REVERT: D 853 PHE cc_start: 0.7373 (m-80) cc_final: 0.6859 (m-80) REVERT: D 864 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5064 (tp30) REVERT: D 868 LYS cc_start: 0.6516 (mttm) cc_final: 0.6032 (mtpm) REVERT: D 928 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.7226 (mtm-85) REVERT: D 972 SER cc_start: 0.7397 (t) cc_final: 0.7037 (p) REVERT: D 981 GLU cc_start: 0.7234 (tp30) cc_final: 0.6868 (tt0) REVERT: D 986 LEU cc_start: 0.7233 (mt) cc_final: 0.6967 (mp) REVERT: D 1001 LYS cc_start: 0.6797 (mmtp) cc_final: 0.6493 (mtmm) REVERT: D 1050 ARG cc_start: 0.6609 (ttm-80) cc_final: 0.6216 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6702 (ttmt) cc_final: 0.6462 (tttm) outliers start: 51 outliers final: 22 residues processed: 505 average time/residue: 2.1439 time to fit residues: 1256.5322 Evaluate side-chains 482 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 453 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN B1047 GLN C 460 ASN C 619 ASN C 699 ASN C 829 HIS C 851 GLN D 494 HIS D 687 ASN ** D 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 851 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18244 Z= 0.307 Angle : 0.562 5.478 24712 Z= 0.288 Chirality : 0.038 0.199 2888 Planarity : 0.004 0.058 3020 Dihedral : 5.432 58.439 2380 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.48 % Allowed : 18.85 % Favored : 78.67 % 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: 0.61 (0.18), residues: 2188 helix: 0.69 (0.12), residues: 1656 sheet: -1.48 (0.67), residues: 48 loop : 0.02 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 711 HIS 0.006 0.001 HIS A 719 PHE 0.014 0.002 PHE C 877 TYR 0.016 0.002 TYR B 842 ARG 0.003 0.000 ARG D 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 508 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 460 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 LYS cc_start: 0.7102 (mttt) cc_final: 0.6856 (mmtm) REVERT: A 528 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6224 (mm-40) REVERT: A 544 LEU cc_start: 0.7934 (mt) cc_final: 0.7467 (mm) REVERT: A 547 ASP cc_start: 0.7316 (t0) cc_final: 0.6511 (t0) REVERT: A 562 LYS cc_start: 0.7358 (mmtt) cc_final: 0.7109 (ttmm) REVERT: A 591 LYS cc_start: 0.7785 (mttt) cc_final: 0.7379 (mttm) REVERT: A 603 LYS cc_start: 0.8300 (mttt) cc_final: 0.8038 (tttm) REVERT: A 606 ASP cc_start: 0.7739 (m-30) cc_final: 0.6729 (p0) REVERT: A 640 PHE cc_start: 0.6340 (m-80) cc_final: 0.5486 (m-10) REVERT: A 642 MET cc_start: 0.6549 (mtm) cc_final: 0.6314 (mtm) REVERT: A 664 GLN cc_start: 0.7620 (pt0) cc_final: 0.7298 (tp40) REVERT: A 699 ASN cc_start: 0.7172 (m-40) cc_final: 0.6617 (m110) REVERT: A 704 LYS cc_start: 0.6279 (mttt) cc_final: 0.5531 (mmtp) REVERT: A 720 MET cc_start: 0.6391 (mmm) cc_final: 0.5787 (mmp) REVERT: A 721 MET cc_start: 0.5900 (ttm) cc_final: 0.5507 (tpt) REVERT: A 727 CYS cc_start: 0.6940 (t) cc_final: 0.6614 (m) REVERT: A 744 MET cc_start: 0.6844 (mmt) cc_final: 0.6581 (mmm) REVERT: A 808 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5998 (mt-10) REVERT: A 852 ARG cc_start: 0.6454 (mmt90) cc_final: 0.6070 (mmt-90) REVERT: A 864 GLU cc_start: 0.6488 (tt0) cc_final: 0.5750 (mm-30) REVERT: A 868 LYS cc_start: 0.6237 (mttm) cc_final: 0.5772 (mtpm) REVERT: A 877 PHE cc_start: 0.6552 (m-10) cc_final: 0.5905 (m-80) REVERT: A 882 LEU cc_start: 0.7621 (tp) cc_final: 0.7382 (tp) REVERT: A 912 MET cc_start: 0.7413 (ttp) cc_final: 0.7124 (ttm) REVERT: A 930 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6595 (mt-10) REVERT: A 986 LEU cc_start: 0.7162 (mm) cc_final: 0.6798 (mp) REVERT: A 987 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 1001 LYS cc_start: 0.6916 (mmtp) cc_final: 0.6467 (mtmm) REVERT: A 1052 LYS cc_start: 0.6351 (tttp) cc_final: 0.5968 (mtpp) REVERT: B 481 HIS cc_start: 0.6285 (OUTLIER) cc_final: 0.5733 (m-70) REVERT: B 528 GLN cc_start: 0.6854 (mm-40) cc_final: 0.6586 (mm110) REVERT: B 544 LEU cc_start: 0.7314 (mt) cc_final: 0.6815 (mm) REVERT: B 575 VAL cc_start: 0.8363 (p) cc_final: 0.7945 (m) REVERT: B 593 LYS cc_start: 0.7459 (ttpt) cc_final: 0.7018 (tttm) REVERT: B 607 GLU cc_start: 0.6173 (tt0) cc_final: 0.5816 (tt0) REVERT: B 628 GLU cc_start: 0.7472 (tt0) cc_final: 0.6462 (tm-30) REVERT: B 629 TYR cc_start: 0.7636 (m-80) cc_final: 0.7329 (m-80) REVERT: B 634 MET cc_start: 0.7319 (tpt) cc_final: 0.7085 (tpt) REVERT: B 640 PHE cc_start: 0.6300 (m-80) cc_final: 0.5791 (m-10) REVERT: B 642 MET cc_start: 0.6734 (mtp) cc_final: 0.6476 (mtm) REVERT: B 687 ASN cc_start: 0.7437 (m-40) cc_final: 0.6679 (m110) REVERT: B 695 ILE cc_start: 0.7049 (tt) cc_final: 0.6604 (tp) REVERT: B 699 ASN cc_start: 0.7131 (m-40) cc_final: 0.6409 (m110) REVERT: B 704 LYS cc_start: 0.6347 (mttt) cc_final: 0.5590 (mmtm) REVERT: B 721 MET cc_start: 0.6178 (ttm) cc_final: 0.5736 (tpt) REVERT: B 727 CYS cc_start: 0.7664 (t) cc_final: 0.7082 (m) REVERT: B 731 ILE cc_start: 0.7550 (mt) cc_final: 0.7340 (mm) REVERT: B 808 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5954 (mt-10) REVERT: B 864 GLU cc_start: 0.6624 (tt0) cc_final: 0.5766 (tp30) REVERT: B 868 LYS cc_start: 0.6495 (mttm) cc_final: 0.6029 (mtpm) REVERT: B 873 SER cc_start: 0.6528 (t) cc_final: 0.6265 (p) REVERT: B 896 ASP cc_start: 0.7849 (m-30) cc_final: 0.7552 (m-30) REVERT: B 909 PHE cc_start: 0.7425 (t80) cc_final: 0.7167 (t80) REVERT: B 928 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: B 966 ASP cc_start: 0.5502 (m-30) cc_final: 0.5142 (m-30) REVERT: B 972 SER cc_start: 0.7458 (t) cc_final: 0.7021 (p) REVERT: B 981 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6481 (mm-30) REVERT: B 1001 LYS cc_start: 0.7175 (mmtp) cc_final: 0.6761 (mtmm) REVERT: B 1042 MET cc_start: 0.6495 (pp-130) cc_final: 0.6248 (pp-130) REVERT: B 1052 LYS cc_start: 0.6447 (ttmt) cc_final: 0.6166 (ttmm) REVERT: B 1063 GLU cc_start: 0.7132 (tp30) cc_final: 0.6690 (mm-30) REVERT: B 1073 GLU cc_start: 0.7805 (tt0) cc_final: 0.7468 (tp30) REVERT: C 496 LYS cc_start: 0.7023 (mttt) cc_final: 0.6802 (mptm) REVERT: C 504 LYS cc_start: 0.6824 (mmtm) cc_final: 0.6569 (mtpp) REVERT: C 528 GLN cc_start: 0.6479 (mm-40) cc_final: 0.6130 (mm-40) REVERT: C 544 LEU cc_start: 0.7883 (mt) cc_final: 0.7458 (mm) REVERT: C 569 SER cc_start: 0.6971 (t) cc_final: 0.6674 (m) REVERT: C 571 ASN cc_start: 0.8209 (m110) cc_final: 0.7587 (t0) REVERT: C 606 ASP cc_start: 0.7455 (m-30) cc_final: 0.6347 (p0) REVERT: C 628 GLU cc_start: 0.7137 (tt0) cc_final: 0.6584 (tt0) REVERT: C 640 PHE cc_start: 0.6339 (m-80) cc_final: 0.5610 (m-10) REVERT: C 689 MET cc_start: 0.7903 (mtt) cc_final: 0.7617 (mtt) REVERT: C 691 GLN cc_start: 0.7564 (mt0) cc_final: 0.6964 (mm-40) REVERT: C 699 ASN cc_start: 0.7168 (m110) cc_final: 0.6917 (m110) REVERT: C 720 MET cc_start: 0.6337 (mmm) cc_final: 0.5774 (mmp) REVERT: C 721 MET cc_start: 0.6150 (ttm) cc_final: 0.5691 (tpp) REVERT: C 727 CYS cc_start: 0.7454 (t) cc_final: 0.6779 (m) REVERT: C 731 ILE cc_start: 0.7894 (mt) cc_final: 0.7640 (mm) REVERT: C 808 GLU cc_start: 0.6413 (mt-10) cc_final: 0.6152 (mt-10) REVERT: C 854 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6622 (mt-10) REVERT: C 864 GLU cc_start: 0.6433 (tt0) cc_final: 0.5694 (tp30) REVERT: C 868 LYS cc_start: 0.6277 (mttm) cc_final: 0.5719 (mtmp) REVERT: C 920 GLU cc_start: 0.7137 (tt0) cc_final: 0.6516 (tt0) REVERT: C 972 SER cc_start: 0.7639 (t) cc_final: 0.7271 (p) REVERT: C 986 LEU cc_start: 0.7713 (mm) cc_final: 0.7439 (mp) REVERT: C 987 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6877 (mm-30) REVERT: C 1001 LYS cc_start: 0.7054 (mmtp) cc_final: 0.6665 (mtmm) REVERT: C 1046 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7207 (mtpp) REVERT: C 1050 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6861 (ttt-90) REVERT: D 504 LYS cc_start: 0.6779 (mmtm) cc_final: 0.6515 (mtpp) REVERT: D 528 GLN cc_start: 0.6450 (mm-40) cc_final: 0.5777 (mm-40) REVERT: D 544 LEU cc_start: 0.7694 (mt) cc_final: 0.7304 (mt) REVERT: D 562 LYS cc_start: 0.6852 (mttt) cc_final: 0.6612 (ttmm) REVERT: D 575 VAL cc_start: 0.8353 (p) cc_final: 0.7947 (m) REVERT: D 593 LYS cc_start: 0.7443 (ttpt) cc_final: 0.7109 (tttm) REVERT: D 603 LYS cc_start: 0.8250 (mttt) cc_final: 0.7865 (tmmt) REVERT: D 606 ASP cc_start: 0.7540 (m-30) cc_final: 0.6345 (p0) REVERT: D 628 GLU cc_start: 0.7136 (tt0) cc_final: 0.6193 (tm-30) REVERT: D 640 PHE cc_start: 0.6196 (m-80) cc_final: 0.5626 (m-10) REVERT: D 699 ASN cc_start: 0.6848 (m-40) cc_final: 0.6072 (m-40) REVERT: D 704 LYS cc_start: 0.5944 (mttt) cc_final: 0.4948 (mmpt) REVERT: D 717 ARG cc_start: 0.6220 (ttt180) cc_final: 0.5944 (ttm-80) REVERT: D 720 MET cc_start: 0.6410 (mmm) cc_final: 0.5600 (mmp) REVERT: D 727 CYS cc_start: 0.7436 (t) cc_final: 0.7017 (m) REVERT: D 852 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6326 (mmt90) REVERT: D 853 PHE cc_start: 0.7342 (m-80) cc_final: 0.6891 (m-80) REVERT: D 864 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5131 (tp30) REVERT: D 868 LYS cc_start: 0.6482 (mttm) cc_final: 0.6074 (mtpm) REVERT: D 911 MET cc_start: 0.8116 (mtp) cc_final: 0.7866 (mtm) REVERT: D 930 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6090 (mt-10) REVERT: D 972 SER cc_start: 0.7359 (t) cc_final: 0.7037 (p) REVERT: D 981 GLU cc_start: 0.7299 (tp30) cc_final: 0.6958 (tt0) REVERT: D 986 LEU cc_start: 0.7194 (mt) cc_final: 0.6938 (mp) REVERT: D 1001 LYS cc_start: 0.6884 (mmtp) cc_final: 0.6558 (mtmm) REVERT: D 1004 ILE cc_start: 0.7229 (mp) cc_final: 0.6834 (mt) REVERT: D 1050 ARG cc_start: 0.6643 (ttm-80) cc_final: 0.6243 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6685 (ttmt) cc_final: 0.6376 (ttmm) REVERT: D 1059 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5891 (mm-30) outliers start: 48 outliers final: 23 residues processed: 492 average time/residue: 2.2275 time to fit residues: 1264.7778 Evaluate side-chains 478 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 450 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 1059 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 0.0010 chunk 158 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 HIS C 851 GLN D 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18244 Z= 0.235 Angle : 0.527 5.790 24712 Z= 0.267 Chirality : 0.037 0.180 2888 Planarity : 0.004 0.061 3020 Dihedral : 5.028 57.411 2376 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.63 % Allowed : 19.32 % Favored : 78.05 % 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: 1.00 (0.18), residues: 2188 helix: 1.00 (0.13), residues: 1656 sheet: -1.56 (0.67), residues: 48 loop : 0.07 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 711 HIS 0.005 0.001 HIS A 719 PHE 0.016 0.001 PHE C 877 TYR 0.025 0.001 TYR C 842 ARG 0.008 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 513 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 462 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6203 (mm-40) REVERT: A 544 LEU cc_start: 0.7905 (mt) cc_final: 0.7434 (mm) REVERT: A 562 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7112 (ttmm) REVERT: A 591 LYS cc_start: 0.7732 (mttt) cc_final: 0.7333 (mttm) REVERT: A 603 LYS cc_start: 0.8285 (mttt) cc_final: 0.8036 (tttm) REVERT: A 606 ASP cc_start: 0.7731 (m-30) cc_final: 0.6684 (p0) REVERT: A 640 PHE cc_start: 0.6412 (m-80) cc_final: 0.5506 (m-10) REVERT: A 642 MET cc_start: 0.6546 (mtm) cc_final: 0.6321 (mtm) REVERT: A 664 GLN cc_start: 0.7650 (pt0) cc_final: 0.7320 (tp40) REVERT: A 699 ASN cc_start: 0.7134 (m-40) cc_final: 0.6591 (m110) REVERT: A 704 LYS cc_start: 0.6172 (mttt) cc_final: 0.5395 (mmtp) REVERT: A 720 MET cc_start: 0.6372 (mmm) cc_final: 0.5836 (mmp) REVERT: A 721 MET cc_start: 0.5891 (ttm) cc_final: 0.5487 (tpt) REVERT: A 744 MET cc_start: 0.6886 (mmt) cc_final: 0.6602 (mmm) REVERT: A 808 GLU cc_start: 0.6344 (mt-10) cc_final: 0.6042 (mt-10) REVERT: A 852 ARG cc_start: 0.6438 (mmt90) cc_final: 0.6044 (mmt-90) REVERT: A 864 GLU cc_start: 0.6410 (tt0) cc_final: 0.5705 (mm-30) REVERT: A 868 LYS cc_start: 0.6196 (mttm) cc_final: 0.5765 (mtpm) REVERT: A 877 PHE cc_start: 0.6512 (m-10) cc_final: 0.5798 (m-80) REVERT: A 912 MET cc_start: 0.7395 (ttp) cc_final: 0.7114 (ttt) REVERT: A 928 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7091 (mtm-85) REVERT: A 930 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6110 (mm-30) REVERT: A 986 LEU cc_start: 0.7267 (mm) cc_final: 0.6886 (mp) REVERT: A 1001 LYS cc_start: 0.6884 (mmtp) cc_final: 0.6420 (mtmm) REVERT: A 1046 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7370 (mtpp) REVERT: A 1050 ARG cc_start: 0.7004 (ttt90) cc_final: 0.6703 (ttm-80) REVERT: A 1052 LYS cc_start: 0.6317 (tttp) cc_final: 0.5946 (mtpp) REVERT: B 481 HIS cc_start: 0.6260 (OUTLIER) cc_final: 0.5706 (m-70) REVERT: B 528 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6596 (mm110) REVERT: B 544 LEU cc_start: 0.7316 (mt) cc_final: 0.6802 (mm) REVERT: B 575 VAL cc_start: 0.8435 (p) cc_final: 0.8014 (m) REVERT: B 593 LYS cc_start: 0.7531 (ttpt) cc_final: 0.7092 (tttm) REVERT: B 607 GLU cc_start: 0.6157 (tt0) cc_final: 0.5851 (tt0) REVERT: B 628 GLU cc_start: 0.7436 (tt0) cc_final: 0.6405 (tm-30) REVERT: B 629 TYR cc_start: 0.7554 (m-80) cc_final: 0.7291 (m-80) REVERT: B 634 MET cc_start: 0.7338 (tpt) cc_final: 0.7098 (tpt) REVERT: B 640 PHE cc_start: 0.6297 (m-80) cc_final: 0.5766 (m-10) REVERT: B 642 MET cc_start: 0.6793 (mtp) cc_final: 0.6387 (mtm) REVERT: B 687 ASN cc_start: 0.7331 (m-40) cc_final: 0.6597 (m110) REVERT: B 695 ILE cc_start: 0.6966 (tt) cc_final: 0.6484 (tp) REVERT: B 699 ASN cc_start: 0.7089 (m-40) cc_final: 0.6366 (m110) REVERT: B 704 LYS cc_start: 0.6346 (mttt) cc_final: 0.5590 (mmtm) REVERT: B 721 MET cc_start: 0.6189 (ttm) cc_final: 0.5776 (tpt) REVERT: B 727 CYS cc_start: 0.7642 (t) cc_final: 0.7070 (m) REVERT: B 808 GLU cc_start: 0.6279 (mt-10) cc_final: 0.5953 (mt-10) REVERT: B 864 GLU cc_start: 0.6733 (tt0) cc_final: 0.5851 (mm-30) REVERT: B 868 LYS cc_start: 0.6501 (mttm) cc_final: 0.6000 (mtpm) REVERT: B 873 SER cc_start: 0.6468 (t) cc_final: 0.6140 (p) REVERT: B 874 THR cc_start: 0.7689 (t) cc_final: 0.7082 (p) REVERT: B 896 ASP cc_start: 0.7872 (m-30) cc_final: 0.7617 (m-30) REVERT: B 909 PHE cc_start: 0.7530 (t80) cc_final: 0.7301 (t80) REVERT: B 928 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.7009 (mtm-85) REVERT: B 966 ASP cc_start: 0.5501 (m-30) cc_final: 0.5163 (m-30) REVERT: B 972 SER cc_start: 0.7442 (t) cc_final: 0.6998 (p) REVERT: B 981 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6484 (mm-30) REVERT: B 1001 LYS cc_start: 0.7174 (mmtp) cc_final: 0.6746 (mtmm) REVERT: B 1042 MET cc_start: 0.6545 (pp-130) cc_final: 0.6320 (pp-130) REVERT: B 1052 LYS cc_start: 0.6362 (ttmt) cc_final: 0.6091 (ttmm) REVERT: B 1063 GLU cc_start: 0.7088 (tp30) cc_final: 0.6656 (mm-30) REVERT: C 475 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7378 (tt) REVERT: C 481 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6635 (m-70) REVERT: C 496 LYS cc_start: 0.7025 (mttt) cc_final: 0.6792 (mptm) REVERT: C 504 LYS cc_start: 0.6843 (mmtm) cc_final: 0.6591 (mtpp) REVERT: C 528 GLN cc_start: 0.6451 (mm-40) cc_final: 0.6082 (mm-40) REVERT: C 544 LEU cc_start: 0.7884 (mt) cc_final: 0.7455 (mm) REVERT: C 569 SER cc_start: 0.7057 (t) cc_final: 0.6720 (m) REVERT: C 571 ASN cc_start: 0.8197 (m110) cc_final: 0.7590 (t0) REVERT: C 576 LEU cc_start: 0.8359 (mp) cc_final: 0.7884 (mm) REVERT: C 606 ASP cc_start: 0.7458 (m-30) cc_final: 0.6354 (p0) REVERT: C 628 GLU cc_start: 0.7042 (tt0) cc_final: 0.6500 (tt0) REVERT: C 639 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: C 640 PHE cc_start: 0.6324 (m-80) cc_final: 0.5628 (m-10) REVERT: C 689 MET cc_start: 0.7936 (mtt) cc_final: 0.7550 (mtt) REVERT: C 691 GLN cc_start: 0.7288 (mt0) cc_final: 0.6704 (mm-40) REVERT: C 699 ASN cc_start: 0.7112 (m110) cc_final: 0.6873 (m110) REVERT: C 720 MET cc_start: 0.6357 (mmm) cc_final: 0.5758 (mmp) REVERT: C 721 MET cc_start: 0.6138 (ttm) cc_final: 0.5655 (tpp) REVERT: C 727 CYS cc_start: 0.7451 (t) cc_final: 0.6765 (m) REVERT: C 731 ILE cc_start: 0.7936 (mt) cc_final: 0.7701 (mm) REVERT: C 808 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6186 (mt-10) REVERT: C 864 GLU cc_start: 0.6428 (tt0) cc_final: 0.5633 (tp30) REVERT: C 868 LYS cc_start: 0.6271 (mttm) cc_final: 0.5720 (mtmp) REVERT: C 911 MET cc_start: 0.8119 (mtm) cc_final: 0.7825 (mtm) REVERT: C 912 MET cc_start: 0.7524 (ttp) cc_final: 0.7263 (ttt) REVERT: C 920 GLU cc_start: 0.7102 (tt0) cc_final: 0.6540 (tt0) REVERT: C 972 SER cc_start: 0.7603 (t) cc_final: 0.7224 (p) REVERT: C 986 LEU cc_start: 0.7754 (mm) cc_final: 0.7461 (mp) REVERT: C 987 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6669 (mm-30) REVERT: C 1001 LYS cc_start: 0.7019 (mmtp) cc_final: 0.6631 (mtmm) REVERT: C 1046 LYS cc_start: 0.7375 (ttmt) cc_final: 0.7045 (mtpp) REVERT: C 1050 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6873 (ttt-90) REVERT: D 528 GLN cc_start: 0.6471 (mm-40) cc_final: 0.5795 (mm-40) REVERT: D 562 LYS cc_start: 0.6821 (mttt) cc_final: 0.6593 (ttmm) REVERT: D 575 VAL cc_start: 0.8348 (p) cc_final: 0.7943 (m) REVERT: D 593 LYS cc_start: 0.7518 (ttpt) cc_final: 0.7168 (tttm) REVERT: D 603 LYS cc_start: 0.8245 (mttt) cc_final: 0.7851 (tmmt) REVERT: D 606 ASP cc_start: 0.7534 (m-30) cc_final: 0.6367 (p0) REVERT: D 628 GLU cc_start: 0.7154 (tt0) cc_final: 0.6169 (tm-30) REVERT: D 640 PHE cc_start: 0.6203 (m-80) cc_final: 0.5626 (m-10) REVERT: D 699 ASN cc_start: 0.7080 (m-40) cc_final: 0.6265 (m-40) REVERT: D 704 LYS cc_start: 0.5965 (mttt) cc_final: 0.4955 (mmpt) REVERT: D 717 ARG cc_start: 0.6214 (ttt180) cc_final: 0.5835 (ttp-170) REVERT: D 720 MET cc_start: 0.6383 (mmm) cc_final: 0.5567 (mmp) REVERT: D 727 CYS cc_start: 0.7428 (t) cc_final: 0.7070 (m) REVERT: D 733 MET cc_start: 0.6887 (tpp) cc_final: 0.6669 (tpt) REVERT: D 852 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6241 (mmt90) REVERT: D 853 PHE cc_start: 0.7287 (m-80) cc_final: 0.6836 (m-80) REVERT: D 864 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.5147 (tp30) REVERT: D 868 LYS cc_start: 0.6357 (mttm) cc_final: 0.5945 (mtpm) REVERT: D 873 SER cc_start: 0.7005 (t) cc_final: 0.6748 (p) REVERT: D 930 GLU cc_start: 0.6416 (mt-10) cc_final: 0.6105 (mt-10) REVERT: D 972 SER cc_start: 0.7377 (t) cc_final: 0.7090 (p) REVERT: D 981 GLU cc_start: 0.7253 (tp30) cc_final: 0.6918 (tt0) REVERT: D 986 LEU cc_start: 0.7230 (mt) cc_final: 0.6959 (mp) REVERT: D 995 LEU cc_start: 0.7608 (mm) cc_final: 0.7382 (mm) REVERT: D 1001 LYS cc_start: 0.6929 (mmtp) cc_final: 0.6582 (mtmm) REVERT: D 1004 ILE cc_start: 0.7276 (mp) cc_final: 0.6900 (mt) REVERT: D 1050 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6325 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6674 (ttmt) cc_final: 0.6350 (ttmm) outliers start: 51 outliers final: 22 residues processed: 492 average time/residue: 2.2017 time to fit residues: 1252.3450 Evaluate side-chains 480 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 451 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 1047 GLN Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 829 HIS C 851 GLN D 579 GLN D 664 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18244 Z= 0.225 Angle : 0.517 6.379 24712 Z= 0.261 Chirality : 0.036 0.171 2888 Planarity : 0.004 0.047 3020 Dihedral : 4.881 57.593 2376 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.27 % Allowed : 20.25 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2188 helix: 1.19 (0.13), residues: 1652 sheet: -1.61 (0.66), residues: 48 loop : 0.08 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 711 HIS 0.006 0.001 HIS A 719 PHE 0.013 0.001 PHE C 877 TYR 0.031 0.001 TYR C 842 ARG 0.007 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 502 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 458 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 LEU cc_start: 0.7873 (mt) cc_final: 0.7419 (mm) REVERT: A 562 LYS cc_start: 0.7341 (mmtt) cc_final: 0.7116 (ttmm) REVERT: A 591 LYS cc_start: 0.7662 (mttt) cc_final: 0.7263 (mttm) REVERT: A 603 LYS cc_start: 0.8260 (mttt) cc_final: 0.8047 (tttt) REVERT: A 606 ASP cc_start: 0.7698 (m-30) cc_final: 0.6607 (p0) REVERT: A 640 PHE cc_start: 0.6427 (m-80) cc_final: 0.5493 (m-10) REVERT: A 664 GLN cc_start: 0.7602 (pt0) cc_final: 0.7338 (tp40) REVERT: A 691 GLN cc_start: 0.7186 (mt0) cc_final: 0.6962 (mt0) REVERT: A 699 ASN cc_start: 0.7122 (m-40) cc_final: 0.6578 (m110) REVERT: A 704 LYS cc_start: 0.6166 (mttt) cc_final: 0.5392 (mmtp) REVERT: A 720 MET cc_start: 0.6391 (mmm) cc_final: 0.5820 (mmp) REVERT: A 721 MET cc_start: 0.6036 (ttm) cc_final: 0.5621 (tpt) REVERT: A 744 MET cc_start: 0.6882 (mmt) cc_final: 0.6598 (mmm) REVERT: A 808 GLU cc_start: 0.6336 (mt-10) cc_final: 0.6034 (mt-10) REVERT: A 852 ARG cc_start: 0.6439 (mmt90) cc_final: 0.6031 (mmt-90) REVERT: A 864 GLU cc_start: 0.6401 (tt0) cc_final: 0.5661 (mm-30) REVERT: A 868 LYS cc_start: 0.6203 (mttm) cc_final: 0.5752 (mtpm) REVERT: A 877 PHE cc_start: 0.6454 (m-10) cc_final: 0.5718 (m-80) REVERT: A 912 MET cc_start: 0.7360 (ttp) cc_final: 0.7054 (ttt) REVERT: A 928 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7095 (mtm-85) REVERT: A 930 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6091 (mm-30) REVERT: A 986 LEU cc_start: 0.7318 (mm) cc_final: 0.6926 (mp) REVERT: A 1001 LYS cc_start: 0.6832 (mmtp) cc_final: 0.6360 (mtmm) REVERT: A 1042 MET cc_start: 0.6466 (ppp) cc_final: 0.6143 (pp-130) REVERT: A 1046 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7394 (mtpp) REVERT: A 1052 LYS cc_start: 0.6261 (tttp) cc_final: 0.5863 (mtpp) REVERT: B 481 HIS cc_start: 0.6240 (OUTLIER) cc_final: 0.5668 (m-70) REVERT: B 483 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7396 (mmm) REVERT: B 528 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6613 (mm110) REVERT: B 544 LEU cc_start: 0.7379 (mt) cc_final: 0.6865 (mm) REVERT: B 575 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8048 (m) REVERT: B 593 LYS cc_start: 0.7416 (ttpt) cc_final: 0.6969 (tttm) REVERT: B 607 GLU cc_start: 0.6161 (tt0) cc_final: 0.5893 (tt0) REVERT: B 628 GLU cc_start: 0.7440 (tt0) cc_final: 0.6447 (tm-30) REVERT: B 629 TYR cc_start: 0.7542 (m-80) cc_final: 0.7325 (m-80) REVERT: B 634 MET cc_start: 0.7369 (tpt) cc_final: 0.7120 (tpt) REVERT: B 640 PHE cc_start: 0.6301 (m-80) cc_final: 0.5787 (m-10) REVERT: B 642 MET cc_start: 0.6751 (mtp) cc_final: 0.6399 (mtm) REVERT: B 687 ASN cc_start: 0.7334 (m-40) cc_final: 0.6620 (m110) REVERT: B 695 ILE cc_start: 0.7034 (tt) cc_final: 0.6539 (tp) REVERT: B 699 ASN cc_start: 0.7069 (m-40) cc_final: 0.6359 (m110) REVERT: B 704 LYS cc_start: 0.6360 (mttt) cc_final: 0.5605 (mmtm) REVERT: B 721 MET cc_start: 0.6183 (ttm) cc_final: 0.5765 (tpt) REVERT: B 727 CYS cc_start: 0.7745 (t) cc_final: 0.7002 (m) REVERT: B 842 TYR cc_start: 0.7673 (m-80) cc_final: 0.7470 (m-80) REVERT: B 864 GLU cc_start: 0.6744 (tt0) cc_final: 0.5774 (mm-30) REVERT: B 868 LYS cc_start: 0.6473 (mttm) cc_final: 0.6001 (mtpm) REVERT: B 873 SER cc_start: 0.6451 (t) cc_final: 0.6143 (p) REVERT: B 896 ASP cc_start: 0.7903 (m-30) cc_final: 0.7638 (m-30) REVERT: B 909 PHE cc_start: 0.7329 (t80) cc_final: 0.7094 (t80) REVERT: B 966 ASP cc_start: 0.5504 (m-30) cc_final: 0.5169 (m-30) REVERT: B 972 SER cc_start: 0.7420 (t) cc_final: 0.6982 (p) REVERT: B 981 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6322 (tp30) REVERT: B 1001 LYS cc_start: 0.7167 (mmtp) cc_final: 0.6729 (mtmm) REVERT: B 1042 MET cc_start: 0.6577 (pp-130) cc_final: 0.6218 (pp-130) REVERT: B 1046 LYS cc_start: 0.7323 (ttmt) cc_final: 0.7040 (mtpp) REVERT: B 1052 LYS cc_start: 0.6351 (ttmt) cc_final: 0.6064 (ttmm) REVERT: B 1063 GLU cc_start: 0.6977 (tp30) cc_final: 0.6544 (mm-30) REVERT: C 481 HIS cc_start: 0.7025 (OUTLIER) cc_final: 0.6634 (m-70) REVERT: C 496 LYS cc_start: 0.7027 (mttt) cc_final: 0.6807 (mptm) REVERT: C 504 LYS cc_start: 0.6985 (mmtm) cc_final: 0.6735 (mtpp) REVERT: C 528 GLN cc_start: 0.6482 (mm-40) cc_final: 0.6207 (mm-40) REVERT: C 530 MET cc_start: 0.8053 (mtm) cc_final: 0.7656 (mtp) REVERT: C 544 LEU cc_start: 0.7869 (mt) cc_final: 0.7431 (mm) REVERT: C 569 SER cc_start: 0.7242 (t) cc_final: 0.6910 (m) REVERT: C 571 ASN cc_start: 0.8154 (m110) cc_final: 0.7554 (t0) REVERT: C 576 LEU cc_start: 0.8359 (mp) cc_final: 0.7917 (mm) REVERT: C 606 ASP cc_start: 0.7536 (m-30) cc_final: 0.6425 (p0) REVERT: C 628 GLU cc_start: 0.7107 (tt0) cc_final: 0.6591 (tt0) REVERT: C 639 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: C 640 PHE cc_start: 0.6327 (m-80) cc_final: 0.5632 (m-10) REVERT: C 687 ASN cc_start: 0.7421 (m-40) cc_final: 0.7079 (m110) REVERT: C 689 MET cc_start: 0.7946 (mtt) cc_final: 0.7575 (mtt) REVERT: C 691 GLN cc_start: 0.7310 (mt0) cc_final: 0.6800 (mm-40) REVERT: C 699 ASN cc_start: 0.7133 (m110) cc_final: 0.6920 (m110) REVERT: C 720 MET cc_start: 0.6331 (mmm) cc_final: 0.5718 (mmp) REVERT: C 721 MET cc_start: 0.6028 (ttm) cc_final: 0.5567 (tpp) REVERT: C 727 CYS cc_start: 0.7513 (t) cc_final: 0.6843 (m) REVERT: C 731 ILE cc_start: 0.7909 (mt) cc_final: 0.7693 (mm) REVERT: C 808 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6182 (mt-10) REVERT: C 864 GLU cc_start: 0.6439 (tt0) cc_final: 0.5688 (tp30) REVERT: C 868 LYS cc_start: 0.6259 (mttm) cc_final: 0.5722 (mtmp) REVERT: C 912 MET cc_start: 0.7507 (ttp) cc_final: 0.7253 (ttt) REVERT: C 972 SER cc_start: 0.7577 (t) cc_final: 0.7214 (p) REVERT: C 987 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6724 (mm-30) REVERT: C 1001 LYS cc_start: 0.7014 (mmtp) cc_final: 0.6627 (mtmm) REVERT: C 1046 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7143 (mtpp) REVERT: C 1047 GLN cc_start: 0.6069 (OUTLIER) cc_final: 0.5869 (tt0) REVERT: C 1050 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6823 (ttt-90) REVERT: C 1052 LYS cc_start: 0.6393 (mtpp) cc_final: 0.6103 (mtpm) REVERT: D 483 MET cc_start: 0.6735 (mtt) cc_final: 0.6508 (mtt) REVERT: D 528 GLN cc_start: 0.6532 (mm-40) cc_final: 0.5827 (mm-40) REVERT: D 562 LYS cc_start: 0.6756 (mttt) cc_final: 0.6541 (ttmm) REVERT: D 575 VAL cc_start: 0.8348 (p) cc_final: 0.7944 (m) REVERT: D 593 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7166 (tttm) REVERT: D 603 LYS cc_start: 0.8229 (mttt) cc_final: 0.7821 (tmmt) REVERT: D 606 ASP cc_start: 0.7520 (m-30) cc_final: 0.6367 (p0) REVERT: D 628 GLU cc_start: 0.7166 (tt0) cc_final: 0.6150 (tm-30) REVERT: D 640 PHE cc_start: 0.6261 (m-80) cc_final: 0.5624 (m-10) REVERT: D 699 ASN cc_start: 0.7065 (m-40) cc_final: 0.6234 (m-40) REVERT: D 704 LYS cc_start: 0.5937 (mttt) cc_final: 0.4954 (mmpt) REVERT: D 717 ARG cc_start: 0.6203 (ttt180) cc_final: 0.5854 (ttp-170) REVERT: D 720 MET cc_start: 0.6457 (mmm) cc_final: 0.5563 (mmp) REVERT: D 727 CYS cc_start: 0.7452 (t) cc_final: 0.7070 (m) REVERT: D 852 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6217 (mmt90) REVERT: D 853 PHE cc_start: 0.7281 (m-80) cc_final: 0.6862 (m-80) REVERT: D 864 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.5142 (tp30) REVERT: D 868 LYS cc_start: 0.6455 (mttm) cc_final: 0.6057 (mtpm) REVERT: D 930 GLU cc_start: 0.6356 (mt-10) cc_final: 0.6104 (mt-10) REVERT: D 972 SER cc_start: 0.7360 (t) cc_final: 0.7110 (p) REVERT: D 981 GLU cc_start: 0.7280 (tp30) cc_final: 0.6913 (tt0) REVERT: D 995 LEU cc_start: 0.7582 (mm) cc_final: 0.7346 (mm) REVERT: D 1004 ILE cc_start: 0.7283 (mp) cc_final: 0.6914 (mt) REVERT: D 1050 ARG cc_start: 0.6684 (ttm-80) cc_final: 0.6341 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6687 (ttmt) cc_final: 0.6359 (ttmm) outliers start: 44 outliers final: 21 residues processed: 485 average time/residue: 2.2210 time to fit residues: 1249.5236 Evaluate side-chains 475 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 445 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 639 ASP Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 1047 GLN Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 920 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 HIS C 829 HIS C 851 GLN D 579 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18244 Z= 0.227 Angle : 0.519 6.900 24712 Z= 0.262 Chirality : 0.036 0.166 2888 Planarity : 0.004 0.046 3020 Dihedral : 4.813 57.632 2376 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.17 % Allowed : 20.82 % Favored : 77.01 % 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: 1.32 (0.18), residues: 2188 helix: 1.26 (0.13), residues: 1652 sheet: -1.58 (0.66), residues: 48 loop : 0.08 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 711 HIS 0.005 0.001 HIS A 719 PHE 0.015 0.001 PHE D 877 TYR 0.028 0.001 TYR C 842 ARG 0.004 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 498 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 456 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 LEU cc_start: 0.7755 (mt) cc_final: 0.7234 (mm) REVERT: A 562 LYS cc_start: 0.7340 (mmtt) cc_final: 0.7113 (ttmm) REVERT: A 591 LYS cc_start: 0.7674 (mttt) cc_final: 0.7281 (mttm) REVERT: A 603 LYS cc_start: 0.8269 (mttt) cc_final: 0.8025 (tttm) REVERT: A 606 ASP cc_start: 0.7744 (m-30) cc_final: 0.6618 (p0) REVERT: A 640 PHE cc_start: 0.6429 (m-80) cc_final: 0.5504 (m-10) REVERT: A 664 GLN cc_start: 0.7632 (pt0) cc_final: 0.7324 (tp40) REVERT: A 704 LYS cc_start: 0.6172 (mttt) cc_final: 0.5393 (mmtp) REVERT: A 720 MET cc_start: 0.6356 (mmm) cc_final: 0.5775 (mmp) REVERT: A 721 MET cc_start: 0.6036 (ttm) cc_final: 0.5619 (tpt) REVERT: A 744 MET cc_start: 0.6893 (mmt) cc_final: 0.6602 (mmm) REVERT: A 808 GLU cc_start: 0.6336 (mt-10) cc_final: 0.6043 (mt-10) REVERT: A 852 ARG cc_start: 0.6456 (mmt90) cc_final: 0.6050 (mmt-90) REVERT: A 864 GLU cc_start: 0.6373 (tt0) cc_final: 0.5696 (tp30) REVERT: A 868 LYS cc_start: 0.6200 (mttm) cc_final: 0.5752 (mtpm) REVERT: A 877 PHE cc_start: 0.6506 (m-10) cc_final: 0.5743 (m-80) REVERT: A 912 MET cc_start: 0.7397 (ttp) cc_final: 0.7093 (ttt) REVERT: A 928 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7096 (mtm-85) REVERT: A 930 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6121 (mm-30) REVERT: A 986 LEU cc_start: 0.7495 (mm) cc_final: 0.7033 (mp) REVERT: A 1001 LYS cc_start: 0.6817 (mmtp) cc_final: 0.6349 (mtmm) REVERT: A 1042 MET cc_start: 0.6493 (ppp) cc_final: 0.6212 (pp-130) REVERT: A 1046 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7398 (mtpp) REVERT: A 1050 ARG cc_start: 0.6991 (ttt90) cc_final: 0.6719 (ttm-80) REVERT: A 1052 LYS cc_start: 0.6154 (tttp) cc_final: 0.5759 (mtpp) REVERT: B 481 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5662 (m-70) REVERT: B 483 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7395 (mmm) REVERT: B 528 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6618 (mm110) REVERT: B 571 ASN cc_start: 0.8119 (m110) cc_final: 0.7457 (t0) REVERT: B 575 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8104 (m) REVERT: B 593 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7049 (tttm) REVERT: B 628 GLU cc_start: 0.7483 (tt0) cc_final: 0.6581 (tm-30) REVERT: B 634 MET cc_start: 0.7366 (tpt) cc_final: 0.7117 (tpt) REVERT: B 640 PHE cc_start: 0.6310 (m-80) cc_final: 0.5784 (m-10) REVERT: B 642 MET cc_start: 0.6695 (mtp) cc_final: 0.6371 (mtm) REVERT: B 687 ASN cc_start: 0.7330 (m-40) cc_final: 0.6609 (m110) REVERT: B 695 ILE cc_start: 0.7031 (tt) cc_final: 0.6450 (tp) REVERT: B 698 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6412 (mt) REVERT: B 699 ASN cc_start: 0.7054 (m-40) cc_final: 0.6347 (m110) REVERT: B 704 LYS cc_start: 0.6367 (mttt) cc_final: 0.5613 (mmtm) REVERT: B 721 MET cc_start: 0.6183 (ttm) cc_final: 0.5767 (tpt) REVERT: B 727 CYS cc_start: 0.7729 (t) cc_final: 0.7061 (m) REVERT: B 733 MET cc_start: 0.7191 (tpp) cc_final: 0.6918 (mmm) REVERT: B 842 TYR cc_start: 0.7676 (m-80) cc_final: 0.7448 (m-80) REVERT: B 864 GLU cc_start: 0.6716 (tt0) cc_final: 0.5842 (tp30) REVERT: B 868 LYS cc_start: 0.6436 (mttm) cc_final: 0.5980 (mtpm) REVERT: B 873 SER cc_start: 0.6547 (t) cc_final: 0.6215 (p) REVERT: B 874 THR cc_start: 0.7684 (t) cc_final: 0.7091 (p) REVERT: B 896 ASP cc_start: 0.7894 (m-30) cc_final: 0.7634 (m-30) REVERT: B 909 PHE cc_start: 0.7334 (t80) cc_final: 0.7101 (t80) REVERT: B 966 ASP cc_start: 0.5523 (m-30) cc_final: 0.5221 (m-30) REVERT: B 972 SER cc_start: 0.7422 (t) cc_final: 0.6974 (p) REVERT: B 981 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6381 (tp30) REVERT: B 1001 LYS cc_start: 0.7148 (mmtp) cc_final: 0.6696 (mtmm) REVERT: B 1042 MET cc_start: 0.6555 (pp-130) cc_final: 0.6174 (pp-130) REVERT: B 1046 LYS cc_start: 0.7332 (ttmt) cc_final: 0.7048 (mtpp) REVERT: B 1052 LYS cc_start: 0.6324 (ttmt) cc_final: 0.6003 (ttmm) REVERT: B 1063 GLU cc_start: 0.7022 (tp30) cc_final: 0.6666 (mm-30) REVERT: C 481 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6667 (m-70) REVERT: C 504 LYS cc_start: 0.6982 (mmtm) cc_final: 0.6729 (mtpp) REVERT: C 530 MET cc_start: 0.8081 (mtm) cc_final: 0.7686 (mtp) REVERT: C 544 LEU cc_start: 0.7852 (mt) cc_final: 0.7407 (mm) REVERT: C 569 SER cc_start: 0.7271 (t) cc_final: 0.6941 (m) REVERT: C 571 ASN cc_start: 0.8155 (m110) cc_final: 0.7565 (t0) REVERT: C 606 ASP cc_start: 0.7528 (m-30) cc_final: 0.6415 (p0) REVERT: C 628 GLU cc_start: 0.7126 (tt0) cc_final: 0.6612 (tt0) REVERT: C 640 PHE cc_start: 0.6334 (m-80) cc_final: 0.5619 (m-10) REVERT: C 642 MET cc_start: 0.6595 (mtm) cc_final: 0.6379 (mtm) REVERT: C 687 ASN cc_start: 0.7386 (m-40) cc_final: 0.7043 (m110) REVERT: C 689 MET cc_start: 0.7950 (mtt) cc_final: 0.7589 (mtt) REVERT: C 691 GLN cc_start: 0.7325 (mt0) cc_final: 0.6826 (mm-40) REVERT: C 699 ASN cc_start: 0.7152 (m110) cc_final: 0.6916 (m110) REVERT: C 704 LYS cc_start: 0.6360 (mttt) cc_final: 0.5632 (mmtp) REVERT: C 720 MET cc_start: 0.6338 (mmm) cc_final: 0.5707 (mmp) REVERT: C 721 MET cc_start: 0.6010 (ttm) cc_final: 0.5572 (tpp) REVERT: C 727 CYS cc_start: 0.7488 (t) cc_final: 0.6817 (m) REVERT: C 864 GLU cc_start: 0.6436 (tt0) cc_final: 0.5666 (tp30) REVERT: C 868 LYS cc_start: 0.6247 (mttm) cc_final: 0.5725 (mtmp) REVERT: C 911 MET cc_start: 0.8124 (mtm) cc_final: 0.7877 (mtm) REVERT: C 912 MET cc_start: 0.7507 (ttp) cc_final: 0.7238 (ttt) REVERT: C 972 SER cc_start: 0.7569 (t) cc_final: 0.7236 (p) REVERT: C 986 LEU cc_start: 0.7645 (mm) cc_final: 0.7323 (mp) REVERT: C 987 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6735 (mm-30) REVERT: C 1001 LYS cc_start: 0.7002 (mmtp) cc_final: 0.6617 (mtmm) REVERT: C 1046 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7146 (mtpp) REVERT: C 1050 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6803 (ttt-90) REVERT: C 1052 LYS cc_start: 0.6334 (mtpp) cc_final: 0.5986 (mtpm) REVERT: D 483 MET cc_start: 0.6735 (mtt) cc_final: 0.6511 (mtt) REVERT: D 562 LYS cc_start: 0.6746 (mttt) cc_final: 0.6531 (ttmm) REVERT: D 575 VAL cc_start: 0.8359 (p) cc_final: 0.7960 (m) REVERT: D 593 LYS cc_start: 0.7533 (ttpt) cc_final: 0.7179 (tttm) REVERT: D 603 LYS cc_start: 0.8233 (mttt) cc_final: 0.7828 (tmmt) REVERT: D 606 ASP cc_start: 0.7510 (m-30) cc_final: 0.6365 (p0) REVERT: D 628 GLU cc_start: 0.7151 (tt0) cc_final: 0.6138 (tm-30) REVERT: D 640 PHE cc_start: 0.6071 (m-80) cc_final: 0.5490 (m-10) REVERT: D 699 ASN cc_start: 0.7087 (m-40) cc_final: 0.6269 (m-40) REVERT: D 704 LYS cc_start: 0.5999 (mttt) cc_final: 0.4996 (mmpt) REVERT: D 717 ARG cc_start: 0.6216 (ttt180) cc_final: 0.5851 (ttp-170) REVERT: D 720 MET cc_start: 0.6401 (mmm) cc_final: 0.5512 (mmp) REVERT: D 727 CYS cc_start: 0.7460 (t) cc_final: 0.7062 (m) REVERT: D 852 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6204 (mmt90) REVERT: D 853 PHE cc_start: 0.7272 (m-80) cc_final: 0.6887 (m-80) REVERT: D 864 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.5128 (tp30) REVERT: D 868 LYS cc_start: 0.6316 (mttm) cc_final: 0.5918 (mtpm) REVERT: D 873 SER cc_start: 0.7033 (t) cc_final: 0.6814 (p) REVERT: D 930 GLU cc_start: 0.6347 (mt-10) cc_final: 0.6134 (mt-10) REVERT: D 972 SER cc_start: 0.7373 (t) cc_final: 0.7118 (p) REVERT: D 981 GLU cc_start: 0.7274 (tp30) cc_final: 0.6905 (tt0) REVERT: D 995 LEU cc_start: 0.7584 (mm) cc_final: 0.7346 (mm) REVERT: D 1004 ILE cc_start: 0.7307 (mp) cc_final: 0.6933 (mt) REVERT: D 1050 ARG cc_start: 0.6644 (ttm-80) cc_final: 0.6280 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6635 (ttmt) cc_final: 0.6333 (ttmm) outliers start: 42 outliers final: 19 residues processed: 481 average time/residue: 2.1778 time to fit residues: 1217.1933 Evaluate side-chains 478 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 451 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 829 HIS C 851 GLN C1047 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18244 Z= 0.228 Angle : 0.522 8.130 24712 Z= 0.264 Chirality : 0.036 0.163 2888 Planarity : 0.004 0.043 3020 Dihedral : 4.775 57.563 2376 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.22 % Allowed : 20.71 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2188 helix: 1.28 (0.13), residues: 1652 sheet: -1.51 (0.66), residues: 48 loop : 0.06 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 711 HIS 0.006 0.001 HIS A 719 PHE 0.013 0.001 PHE D 877 TYR 0.025 0.001 TYR C 842 ARG 0.004 0.000 ARG B1050 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 494 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 451 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 LEU cc_start: 0.7828 (mt) cc_final: 0.7270 (mm) REVERT: A 562 LYS cc_start: 0.7346 (mmtt) cc_final: 0.7112 (ttmm) REVERT: A 591 LYS cc_start: 0.7694 (mttt) cc_final: 0.7294 (mttm) REVERT: A 603 LYS cc_start: 0.8274 (mttt) cc_final: 0.8024 (tttm) REVERT: A 606 ASP cc_start: 0.7742 (m-30) cc_final: 0.6620 (p0) REVERT: A 640 PHE cc_start: 0.6423 (m-80) cc_final: 0.5478 (m-10) REVERT: A 664 GLN cc_start: 0.7619 (pt0) cc_final: 0.7324 (tp40) REVERT: A 704 LYS cc_start: 0.6190 (mttt) cc_final: 0.5346 (mmtp) REVERT: A 720 MET cc_start: 0.6344 (mmm) cc_final: 0.5741 (mmp) REVERT: A 721 MET cc_start: 0.6039 (ttm) cc_final: 0.5619 (tpt) REVERT: A 744 MET cc_start: 0.6888 (mmt) cc_final: 0.6588 (mmm) REVERT: A 808 GLU cc_start: 0.6326 (mt-10) cc_final: 0.6038 (mt-10) REVERT: A 852 ARG cc_start: 0.6453 (mmt90) cc_final: 0.6047 (mmt-90) REVERT: A 864 GLU cc_start: 0.6385 (tt0) cc_final: 0.5719 (tp30) REVERT: A 868 LYS cc_start: 0.6146 (mttm) cc_final: 0.5668 (mtpm) REVERT: A 877 PHE cc_start: 0.6503 (m-10) cc_final: 0.5749 (m-80) REVERT: A 912 MET cc_start: 0.7406 (ttp) cc_final: 0.7095 (ttt) REVERT: A 928 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7084 (mtm-85) REVERT: A 930 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6065 (mm-30) REVERT: A 986 LEU cc_start: 0.7401 (mm) cc_final: 0.6935 (mp) REVERT: A 1001 LYS cc_start: 0.6822 (mmtp) cc_final: 0.6351 (mtmm) REVERT: A 1042 MET cc_start: 0.6475 (ppp) cc_final: 0.6149 (pp-130) REVERT: A 1046 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7394 (mtpp) REVERT: A 1050 ARG cc_start: 0.6964 (ttt90) cc_final: 0.6674 (ttm-80) REVERT: A 1052 LYS cc_start: 0.6178 (tttp) cc_final: 0.5781 (mtpp) REVERT: B 481 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5668 (m-70) REVERT: B 483 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7381 (mmm) REVERT: B 528 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6618 (mm110) REVERT: B 571 ASN cc_start: 0.8094 (m110) cc_final: 0.7462 (t0) REVERT: B 575 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8018 (m) REVERT: B 593 LYS cc_start: 0.7504 (ttpt) cc_final: 0.7048 (tttm) REVERT: B 607 GLU cc_start: 0.6129 (tt0) cc_final: 0.5797 (tt0) REVERT: B 628 GLU cc_start: 0.7416 (tt0) cc_final: 0.6427 (tm-30) REVERT: B 634 MET cc_start: 0.7362 (tpt) cc_final: 0.7112 (tpt) REVERT: B 640 PHE cc_start: 0.6392 (m-80) cc_final: 0.5859 (m-10) REVERT: B 642 MET cc_start: 0.6734 (mtp) cc_final: 0.6497 (mtm) REVERT: B 687 ASN cc_start: 0.7332 (m-40) cc_final: 0.6611 (m110) REVERT: B 695 ILE cc_start: 0.7032 (tt) cc_final: 0.6459 (tp) REVERT: B 698 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6441 (mt) REVERT: B 699 ASN cc_start: 0.7059 (m-40) cc_final: 0.6352 (m110) REVERT: B 704 LYS cc_start: 0.6370 (mttt) cc_final: 0.5614 (mmtm) REVERT: B 721 MET cc_start: 0.6172 (ttm) cc_final: 0.5745 (tpt) REVERT: B 727 CYS cc_start: 0.7730 (t) cc_final: 0.7078 (m) REVERT: B 733 MET cc_start: 0.7183 (tpp) cc_final: 0.6917 (mmm) REVERT: B 808 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5938 (mt-10) REVERT: B 864 GLU cc_start: 0.6721 (tt0) cc_final: 0.5840 (tp30) REVERT: B 868 LYS cc_start: 0.6438 (mttm) cc_final: 0.5981 (mtpm) REVERT: B 873 SER cc_start: 0.6540 (t) cc_final: 0.6216 (p) REVERT: B 896 ASP cc_start: 0.7902 (m-30) cc_final: 0.7637 (m-30) REVERT: B 909 PHE cc_start: 0.7334 (t80) cc_final: 0.7059 (t80) REVERT: B 966 ASP cc_start: 0.5525 (m-30) cc_final: 0.5216 (m-30) REVERT: B 972 SER cc_start: 0.7416 (t) cc_final: 0.6973 (p) REVERT: B 981 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6353 (tp30) REVERT: B 1001 LYS cc_start: 0.7151 (mmtp) cc_final: 0.6694 (mtmm) REVERT: B 1042 MET cc_start: 0.6582 (pp-130) cc_final: 0.6201 (pp-130) REVERT: B 1046 LYS cc_start: 0.7321 (ttmt) cc_final: 0.7041 (mtpp) REVERT: B 1052 LYS cc_start: 0.6349 (ttmt) cc_final: 0.6009 (ttmm) REVERT: B 1063 GLU cc_start: 0.7024 (tp30) cc_final: 0.6671 (mm-30) REVERT: C 481 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6693 (m-70) REVERT: C 504 LYS cc_start: 0.6972 (mmtm) cc_final: 0.6719 (mtpp) REVERT: C 528 GLN cc_start: 0.6580 (mm-40) cc_final: 0.6167 (mt0) REVERT: C 530 MET cc_start: 0.8086 (mtm) cc_final: 0.7698 (mtp) REVERT: C 569 SER cc_start: 0.7232 (t) cc_final: 0.6888 (m) REVERT: C 571 ASN cc_start: 0.8158 (m110) cc_final: 0.7561 (t0) REVERT: C 606 ASP cc_start: 0.7547 (m-30) cc_final: 0.6445 (p0) REVERT: C 640 PHE cc_start: 0.6306 (m-80) cc_final: 0.5630 (m-10) REVERT: C 642 MET cc_start: 0.6593 (mtm) cc_final: 0.6378 (mtm) REVERT: C 687 ASN cc_start: 0.7362 (m-40) cc_final: 0.6972 (m110) REVERT: C 689 MET cc_start: 0.7972 (mtt) cc_final: 0.7626 (mtt) REVERT: C 691 GLN cc_start: 0.7321 (mt0) cc_final: 0.6817 (mm-40) REVERT: C 720 MET cc_start: 0.6335 (mmm) cc_final: 0.5684 (mmp) REVERT: C 721 MET cc_start: 0.6021 (ttm) cc_final: 0.5585 (tpp) REVERT: C 727 CYS cc_start: 0.7462 (t) cc_final: 0.6670 (m) REVERT: C 853 PHE cc_start: 0.7985 (m-80) cc_final: 0.7597 (m-80) REVERT: C 864 GLU cc_start: 0.6462 (tt0) cc_final: 0.5629 (tp30) REVERT: C 868 LYS cc_start: 0.6129 (mttm) cc_final: 0.5592 (mtmp) REVERT: C 911 MET cc_start: 0.8106 (mtm) cc_final: 0.7877 (mtm) REVERT: C 912 MET cc_start: 0.7504 (ttp) cc_final: 0.7248 (ttt) REVERT: C 972 SER cc_start: 0.7565 (t) cc_final: 0.7238 (p) REVERT: C 986 LEU cc_start: 0.7602 (mm) cc_final: 0.7250 (mp) REVERT: C 987 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6681 (mm-30) REVERT: C 1001 LYS cc_start: 0.7137 (mmtp) cc_final: 0.6741 (mtmm) REVERT: C 1046 LYS cc_start: 0.7459 (ttmt) cc_final: 0.7143 (mtpp) REVERT: C 1050 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6756 (ttt-90) REVERT: D 483 MET cc_start: 0.6744 (mtt) cc_final: 0.6513 (mtt) REVERT: D 562 LYS cc_start: 0.6743 (mttt) cc_final: 0.6525 (ttmm) REVERT: D 575 VAL cc_start: 0.8358 (p) cc_final: 0.7960 (m) REVERT: D 593 LYS cc_start: 0.7547 (ttpt) cc_final: 0.7193 (tttm) REVERT: D 603 LYS cc_start: 0.8213 (mttt) cc_final: 0.7790 (tmmt) REVERT: D 606 ASP cc_start: 0.7505 (m-30) cc_final: 0.6368 (p0) REVERT: D 628 GLU cc_start: 0.7152 (tt0) cc_final: 0.6126 (tm-30) REVERT: D 640 PHE cc_start: 0.6072 (m-80) cc_final: 0.5475 (m-10) REVERT: D 699 ASN cc_start: 0.7078 (m-40) cc_final: 0.6258 (m-40) REVERT: D 704 LYS cc_start: 0.5942 (mttt) cc_final: 0.4961 (mmpt) REVERT: D 717 ARG cc_start: 0.6230 (ttt180) cc_final: 0.5855 (ttp-170) REVERT: D 720 MET cc_start: 0.6419 (mmm) cc_final: 0.5514 (mmp) REVERT: D 727 CYS cc_start: 0.7472 (t) cc_final: 0.7067 (m) REVERT: D 852 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6236 (mmt90) REVERT: D 853 PHE cc_start: 0.7258 (m-80) cc_final: 0.6866 (m-80) REVERT: D 864 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.5133 (tp30) REVERT: D 868 LYS cc_start: 0.6318 (mttm) cc_final: 0.5920 (mtpm) REVERT: D 873 SER cc_start: 0.7042 (t) cc_final: 0.6755 (p) REVERT: D 930 GLU cc_start: 0.6345 (mt-10) cc_final: 0.6005 (mm-30) REVERT: D 972 SER cc_start: 0.7338 (t) cc_final: 0.7110 (p) REVERT: D 981 GLU cc_start: 0.7255 (tp30) cc_final: 0.6884 (tt0) REVERT: D 995 LEU cc_start: 0.7602 (mm) cc_final: 0.7354 (mm) REVERT: D 1004 ILE cc_start: 0.7298 (mp) cc_final: 0.6930 (mt) REVERT: D 1048 LYS cc_start: 0.6032 (ttpp) cc_final: 0.5813 (ttpp) REVERT: D 1050 ARG cc_start: 0.6657 (ttm-80) cc_final: 0.6299 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6644 (ttmt) cc_final: 0.6322 (ttmm) outliers start: 43 outliers final: 20 residues processed: 478 average time/residue: 2.1872 time to fit residues: 1212.6313 Evaluate side-chains 475 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 447 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 1047 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.9990 chunk 185 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 700 HIS C 851 GLN C1047 GLN D 579 GLN D 699 ASN D 700 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18244 Z= 0.304 Angle : 0.561 8.681 24712 Z= 0.286 Chirality : 0.038 0.166 2888 Planarity : 0.004 0.046 3020 Dihedral : 4.948 58.861 2376 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.01 % Allowed : 21.23 % Favored : 76.76 % 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: 1.05 (0.18), residues: 2188 helix: 1.07 (0.13), residues: 1652 sheet: -1.59 (0.67), residues: 48 loop : -0.06 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 711 HIS 0.006 0.001 HIS A 719 PHE 0.013 0.002 PHE D 877 TYR 0.033 0.002 TYR B 842 ARG 0.004 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 489 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 450 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 LEU cc_start: 0.7805 (mt) cc_final: 0.7228 (mm) REVERT: A 562 LYS cc_start: 0.7351 (mmtt) cc_final: 0.7107 (ttmm) REVERT: A 591 LYS cc_start: 0.7689 (mttt) cc_final: 0.7288 (mttm) REVERT: A 603 LYS cc_start: 0.8292 (mttt) cc_final: 0.8078 (tttt) REVERT: A 606 ASP cc_start: 0.7704 (m-30) cc_final: 0.6598 (p0) REVERT: A 628 GLU cc_start: 0.7023 (tt0) cc_final: 0.6203 (tm-30) REVERT: A 640 PHE cc_start: 0.6591 (m-80) cc_final: 0.5681 (m-10) REVERT: A 642 MET cc_start: 0.6602 (mtm) cc_final: 0.6382 (mtm) REVERT: A 664 GLN cc_start: 0.7686 (pt0) cc_final: 0.7315 (tp40) REVERT: A 704 LYS cc_start: 0.6217 (mttt) cc_final: 0.5413 (mmtp) REVERT: A 720 MET cc_start: 0.6393 (mmm) cc_final: 0.5745 (mmp) REVERT: A 721 MET cc_start: 0.6027 (ttm) cc_final: 0.5613 (tpt) REVERT: A 744 MET cc_start: 0.6876 (mmt) cc_final: 0.6577 (mmm) REVERT: A 808 GLU cc_start: 0.6282 (mt-10) cc_final: 0.6002 (mt-10) REVERT: A 864 GLU cc_start: 0.6403 (tt0) cc_final: 0.5695 (mm-30) REVERT: A 868 LYS cc_start: 0.6177 (mttm) cc_final: 0.5697 (mtpm) REVERT: A 877 PHE cc_start: 0.6560 (m-10) cc_final: 0.5854 (m-80) REVERT: A 912 MET cc_start: 0.7397 (ttp) cc_final: 0.7051 (ttt) REVERT: A 928 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7044 (mtm-85) REVERT: A 930 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6068 (mm-30) REVERT: A 986 LEU cc_start: 0.7402 (mm) cc_final: 0.6962 (mp) REVERT: A 1001 LYS cc_start: 0.6859 (mmtp) cc_final: 0.6403 (mtmm) REVERT: A 1042 MET cc_start: 0.6466 (ppp) cc_final: 0.6120 (pp-130) REVERT: A 1046 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7332 (mtpp) REVERT: A 1052 LYS cc_start: 0.6150 (tttp) cc_final: 0.5752 (mtpp) REVERT: B 481 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.5939 (m-70) REVERT: B 528 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6686 (mm110) REVERT: B 571 ASN cc_start: 0.8147 (m110) cc_final: 0.7512 (t0) REVERT: B 575 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8137 (m) REVERT: B 593 LYS cc_start: 0.7510 (ttpt) cc_final: 0.7050 (tttm) REVERT: B 628 GLU cc_start: 0.7419 (tt0) cc_final: 0.6426 (tm-30) REVERT: B 634 MET cc_start: 0.7304 (tpt) cc_final: 0.7043 (tpt) REVERT: B 640 PHE cc_start: 0.6271 (m-80) cc_final: 0.5734 (m-10) REVERT: B 642 MET cc_start: 0.6726 (mtp) cc_final: 0.6496 (mtm) REVERT: B 687 ASN cc_start: 0.7331 (m-40) cc_final: 0.6578 (m110) REVERT: B 695 ILE cc_start: 0.7011 (tt) cc_final: 0.6422 (tp) REVERT: B 698 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6449 (mt) REVERT: B 699 ASN cc_start: 0.7065 (m-40) cc_final: 0.6331 (m110) REVERT: B 704 LYS cc_start: 0.6322 (mttt) cc_final: 0.5562 (mmtm) REVERT: B 721 MET cc_start: 0.6185 (ttm) cc_final: 0.5775 (tpt) REVERT: B 727 CYS cc_start: 0.7718 (t) cc_final: 0.7106 (m) REVERT: B 864 GLU cc_start: 0.6792 (tt0) cc_final: 0.5869 (tp30) REVERT: B 868 LYS cc_start: 0.6441 (mttm) cc_final: 0.5994 (mtpm) REVERT: B 873 SER cc_start: 0.6543 (t) cc_final: 0.6196 (p) REVERT: B 896 ASP cc_start: 0.7937 (m-30) cc_final: 0.7680 (m-30) REVERT: B 909 PHE cc_start: 0.7374 (t80) cc_final: 0.7106 (t80) REVERT: B 930 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6349 (mt-10) REVERT: B 966 ASP cc_start: 0.5605 (m-30) cc_final: 0.5231 (m-30) REVERT: B 972 SER cc_start: 0.7423 (t) cc_final: 0.6970 (p) REVERT: B 981 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6430 (tp30) REVERT: B 1001 LYS cc_start: 0.7088 (mmtp) cc_final: 0.6676 (mtmm) REVERT: B 1042 MET cc_start: 0.6617 (pp-130) cc_final: 0.6210 (pp-130) REVERT: B 1046 LYS cc_start: 0.7298 (ttmt) cc_final: 0.7017 (mtpp) REVERT: B 1050 ARG cc_start: 0.7032 (ttt90) cc_final: 0.6827 (ttm-80) REVERT: B 1052 LYS cc_start: 0.6339 (ttmt) cc_final: 0.5966 (ttmm) REVERT: B 1063 GLU cc_start: 0.6998 (tp30) cc_final: 0.6582 (mm-30) REVERT: C 481 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6613 (m-70) REVERT: C 504 LYS cc_start: 0.7030 (mmtm) cc_final: 0.6766 (mtpp) REVERT: C 528 GLN cc_start: 0.6560 (mm-40) cc_final: 0.6151 (mt0) REVERT: C 530 MET cc_start: 0.8008 (mtm) cc_final: 0.7612 (mtp) REVERT: C 569 SER cc_start: 0.7251 (t) cc_final: 0.6936 (m) REVERT: C 571 ASN cc_start: 0.8181 (m110) cc_final: 0.7583 (t0) REVERT: C 606 ASP cc_start: 0.7573 (m-30) cc_final: 0.6529 (p0) REVERT: C 640 PHE cc_start: 0.6354 (m-80) cc_final: 0.5648 (m-10) REVERT: C 687 ASN cc_start: 0.7361 (m-40) cc_final: 0.6923 (m110) REVERT: C 689 MET cc_start: 0.7906 (mtt) cc_final: 0.7544 (mtt) REVERT: C 691 GLN cc_start: 0.7316 (mt0) cc_final: 0.6799 (mm-40) REVERT: C 704 LYS cc_start: 0.6334 (mttt) cc_final: 0.5620 (mmtp) REVERT: C 720 MET cc_start: 0.6361 (mmm) cc_final: 0.5727 (mmp) REVERT: C 721 MET cc_start: 0.5985 (ttm) cc_final: 0.5584 (tpp) REVERT: C 727 CYS cc_start: 0.7494 (t) cc_final: 0.6762 (m) REVERT: C 808 GLU cc_start: 0.6418 (mt-10) cc_final: 0.6186 (mt-10) REVERT: C 864 GLU cc_start: 0.6580 (tt0) cc_final: 0.5791 (tp30) REVERT: C 868 LYS cc_start: 0.6137 (mttm) cc_final: 0.5599 (mtmp) REVERT: C 912 MET cc_start: 0.7524 (ttp) cc_final: 0.7236 (ttt) REVERT: C 972 SER cc_start: 0.7596 (t) cc_final: 0.7250 (p) REVERT: C 987 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6815 (mm-30) REVERT: C 1042 MET cc_start: 0.6596 (ppp) cc_final: 0.6333 (pp-130) REVERT: C 1046 LYS cc_start: 0.7470 (ttmt) cc_final: 0.7145 (mtpp) REVERT: C 1050 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7076 (ttt180) REVERT: D 481 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5639 (m-70) REVERT: D 562 LYS cc_start: 0.6697 (mttt) cc_final: 0.6482 (ttmm) REVERT: D 575 VAL cc_start: 0.8360 (p) cc_final: 0.7966 (m) REVERT: D 593 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7207 (tttm) REVERT: D 603 LYS cc_start: 0.8238 (mttt) cc_final: 0.7786 (tmmt) REVERT: D 606 ASP cc_start: 0.7517 (m-30) cc_final: 0.6440 (p0) REVERT: D 628 GLU cc_start: 0.7146 (tt0) cc_final: 0.6142 (tm-30) REVERT: D 640 PHE cc_start: 0.6063 (m-80) cc_final: 0.5465 (m-10) REVERT: D 699 ASN cc_start: 0.6798 (m110) cc_final: 0.6092 (m-40) REVERT: D 704 LYS cc_start: 0.5937 (mttt) cc_final: 0.4971 (mmpt) REVERT: D 717 ARG cc_start: 0.6254 (ttt180) cc_final: 0.5863 (ttp-170) REVERT: D 720 MET cc_start: 0.6467 (mmm) cc_final: 0.5539 (mmp) REVERT: D 727 CYS cc_start: 0.7545 (t) cc_final: 0.7188 (m) REVERT: D 852 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.6134 (mmt90) REVERT: D 853 PHE cc_start: 0.7328 (m-80) cc_final: 0.6885 (m-80) REVERT: D 864 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.5044 (tp30) REVERT: D 868 LYS cc_start: 0.6331 (mttm) cc_final: 0.5912 (mtpm) REVERT: D 873 SER cc_start: 0.7055 (t) cc_final: 0.6786 (p) REVERT: D 930 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6286 (mm-30) REVERT: D 972 SER cc_start: 0.7375 (t) cc_final: 0.7130 (p) REVERT: D 981 GLU cc_start: 0.7259 (tp30) cc_final: 0.6923 (tt0) REVERT: D 995 LEU cc_start: 0.7592 (mm) cc_final: 0.7339 (mm) REVERT: D 1004 ILE cc_start: 0.7298 (mp) cc_final: 0.6935 (mt) REVERT: D 1050 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.6383 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6642 (ttmt) cc_final: 0.6414 (ttmm) outliers start: 39 outliers final: 19 residues processed: 478 average time/residue: 2.1913 time to fit residues: 1218.3490 Evaluate side-chains 468 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 441 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 481 HIS Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 829 HIS C 851 GLN D 579 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18244 Z= 0.196 Angle : 0.520 9.473 24712 Z= 0.263 Chirality : 0.036 0.156 2888 Planarity : 0.004 0.094 3020 Dihedral : 4.745 56.831 2376 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.29 % Allowed : 22.42 % Favored : 76.29 % 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: 1.40 (0.18), residues: 2188 helix: 1.34 (0.13), residues: 1648 sheet: -1.40 (0.69), residues: 48 loop : 0.01 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 711 HIS 0.006 0.001 HIS A 719 PHE 0.012 0.001 PHE D 877 TYR 0.029 0.001 TYR B 842 ARG 0.013 0.000 ARG C 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 443 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 LYS cc_start: 0.7346 (mmtt) cc_final: 0.7102 (ttmm) REVERT: A 591 LYS cc_start: 0.7674 (mttt) cc_final: 0.7304 (mttm) REVERT: A 603 LYS cc_start: 0.8267 (mttt) cc_final: 0.8016 (tttm) REVERT: A 606 ASP cc_start: 0.7750 (m-30) cc_final: 0.6620 (p0) REVERT: A 640 PHE cc_start: 0.6498 (m-80) cc_final: 0.5581 (m-10) REVERT: A 664 GLN cc_start: 0.7662 (pt0) cc_final: 0.7300 (tp40) REVERT: A 704 LYS cc_start: 0.6162 (mttt) cc_final: 0.5389 (mmtp) REVERT: A 720 MET cc_start: 0.6357 (mmm) cc_final: 0.5695 (mmp) REVERT: A 721 MET cc_start: 0.6099 (ttm) cc_final: 0.5650 (tpt) REVERT: A 744 MET cc_start: 0.6845 (mmt) cc_final: 0.6558 (mmm) REVERT: A 808 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5995 (mt-10) REVERT: A 864 GLU cc_start: 0.6478 (tt0) cc_final: 0.5765 (tp30) REVERT: A 868 LYS cc_start: 0.6143 (mttm) cc_final: 0.5676 (mtpm) REVERT: A 877 PHE cc_start: 0.6506 (m-10) cc_final: 0.5775 (m-80) REVERT: A 912 MET cc_start: 0.7412 (ttp) cc_final: 0.7098 (ttt) REVERT: A 928 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7084 (mtm-85) REVERT: A 930 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6115 (mm-30) REVERT: A 986 LEU cc_start: 0.7542 (mm) cc_final: 0.7077 (mp) REVERT: A 1001 LYS cc_start: 0.6873 (mmtp) cc_final: 0.6421 (mtmm) REVERT: A 1042 MET cc_start: 0.6460 (ppp) cc_final: 0.6102 (pp-130) REVERT: A 1046 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7332 (mtpp) REVERT: A 1052 LYS cc_start: 0.6171 (tttp) cc_final: 0.5780 (mtpp) REVERT: B 481 HIS cc_start: 0.6261 (OUTLIER) cc_final: 0.5728 (m-70) REVERT: B 528 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6701 (mm110) REVERT: B 575 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8026 (m) REVERT: B 593 LYS cc_start: 0.7505 (ttpt) cc_final: 0.7049 (tttm) REVERT: B 607 GLU cc_start: 0.6157 (tt0) cc_final: 0.5870 (tt0) REVERT: B 628 GLU cc_start: 0.7457 (tt0) cc_final: 0.6554 (tm-30) REVERT: B 634 MET cc_start: 0.7380 (tpt) cc_final: 0.7125 (tpt) REVERT: B 642 MET cc_start: 0.6708 (mtp) cc_final: 0.6493 (mtm) REVERT: B 687 ASN cc_start: 0.7317 (m-40) cc_final: 0.6544 (m110) REVERT: B 695 ILE cc_start: 0.7002 (tt) cc_final: 0.6426 (tp) REVERT: B 698 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6528 (mt) REVERT: B 699 ASN cc_start: 0.7062 (m-40) cc_final: 0.6353 (m110) REVERT: B 704 LYS cc_start: 0.6376 (mttt) cc_final: 0.5624 (mmtm) REVERT: B 721 MET cc_start: 0.6190 (ttm) cc_final: 0.5750 (tpt) REVERT: B 727 CYS cc_start: 0.7698 (t) cc_final: 0.7114 (m) REVERT: B 733 MET cc_start: 0.7200 (tpp) cc_final: 0.6923 (mmm) REVERT: B 808 GLU cc_start: 0.6293 (mt-10) cc_final: 0.5941 (mt-10) REVERT: B 864 GLU cc_start: 0.6737 (tt0) cc_final: 0.5841 (tp30) REVERT: B 868 LYS cc_start: 0.6437 (mttm) cc_final: 0.5985 (mtpm) REVERT: B 873 SER cc_start: 0.6548 (t) cc_final: 0.6206 (p) REVERT: B 896 ASP cc_start: 0.7917 (m-30) cc_final: 0.7660 (m-30) REVERT: B 909 PHE cc_start: 0.7348 (t80) cc_final: 0.7131 (t80) REVERT: B 930 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6399 (mt-10) REVERT: B 966 ASP cc_start: 0.5562 (m-30) cc_final: 0.5224 (m-30) REVERT: B 972 SER cc_start: 0.7456 (t) cc_final: 0.7010 (p) REVERT: B 981 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6339 (tp30) REVERT: B 1001 LYS cc_start: 0.7107 (mmtp) cc_final: 0.6682 (mtmm) REVERT: B 1042 MET cc_start: 0.6610 (pp-130) cc_final: 0.6171 (pp-130) REVERT: B 1046 LYS cc_start: 0.7303 (ttmt) cc_final: 0.6954 (mtpp) REVERT: B 1050 ARG cc_start: 0.7126 (ttt90) cc_final: 0.6843 (ttm-80) REVERT: B 1052 LYS cc_start: 0.6300 (ttmt) cc_final: 0.6024 (ttmm) REVERT: B 1063 GLU cc_start: 0.6967 (tp30) cc_final: 0.6581 (mm-30) REVERT: C 475 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7343 (tt) REVERT: C 481 HIS cc_start: 0.7107 (OUTLIER) cc_final: 0.6662 (m-70) REVERT: C 504 LYS cc_start: 0.6956 (mmtm) cc_final: 0.6690 (mtpp) REVERT: C 528 GLN cc_start: 0.6588 (mm-40) cc_final: 0.6199 (mt0) REVERT: C 530 MET cc_start: 0.8079 (mtm) cc_final: 0.7689 (mtp) REVERT: C 569 SER cc_start: 0.7222 (t) cc_final: 0.6879 (m) REVERT: C 571 ASN cc_start: 0.8150 (m110) cc_final: 0.7624 (t0) REVERT: C 597 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6265 (mp) REVERT: C 606 ASP cc_start: 0.7566 (m-30) cc_final: 0.6459 (p0) REVERT: C 640 PHE cc_start: 0.6329 (m-80) cc_final: 0.5625 (m-10) REVERT: C 687 ASN cc_start: 0.7345 (m-40) cc_final: 0.6928 (m110) REVERT: C 689 MET cc_start: 0.7928 (mtt) cc_final: 0.7578 (mtt) REVERT: C 691 GLN cc_start: 0.7306 (mt0) cc_final: 0.6827 (mm-40) REVERT: C 699 ASN cc_start: 0.6967 (m110) cc_final: 0.6630 (m110) REVERT: C 720 MET cc_start: 0.6343 (mmm) cc_final: 0.5688 (mmp) REVERT: C 721 MET cc_start: 0.5963 (ttm) cc_final: 0.5542 (tpp) REVERT: C 727 CYS cc_start: 0.7425 (t) cc_final: 0.6785 (m) REVERT: C 808 GLU cc_start: 0.6347 (mt-10) cc_final: 0.6065 (mt-10) REVERT: C 853 PHE cc_start: 0.7983 (m-80) cc_final: 0.7591 (m-80) REVERT: C 864 GLU cc_start: 0.6569 (tt0) cc_final: 0.5787 (tp30) REVERT: C 868 LYS cc_start: 0.6107 (mttm) cc_final: 0.5575 (mtmp) REVERT: C 912 MET cc_start: 0.7530 (ttp) cc_final: 0.7276 (ttt) REVERT: C 972 SER cc_start: 0.7567 (t) cc_final: 0.7245 (p) REVERT: C 986 LEU cc_start: 0.7644 (mm) cc_final: 0.7318 (mp) REVERT: C 987 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6681 (mm-30) REVERT: C 1042 MET cc_start: 0.6538 (ppp) cc_final: 0.6284 (pp-130) REVERT: C 1046 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7124 (mtpp) REVERT: C 1050 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6838 (ttt-90) REVERT: D 483 MET cc_start: 0.6753 (mtt) cc_final: 0.6514 (mtt) REVERT: D 562 LYS cc_start: 0.6730 (mttt) cc_final: 0.6507 (ttmm) REVERT: D 575 VAL cc_start: 0.8244 (p) cc_final: 0.7842 (m) REVERT: D 593 LYS cc_start: 0.7541 (ttpt) cc_final: 0.7177 (tttm) REVERT: D 603 LYS cc_start: 0.8208 (mttt) cc_final: 0.7774 (tmmt) REVERT: D 606 ASP cc_start: 0.7497 (m-30) cc_final: 0.6372 (p0) REVERT: D 628 GLU cc_start: 0.7184 (tt0) cc_final: 0.6166 (tm-30) REVERT: D 640 PHE cc_start: 0.6067 (m-80) cc_final: 0.5450 (m-10) REVERT: D 699 ASN cc_start: 0.6766 (m110) cc_final: 0.6047 (m110) REVERT: D 704 LYS cc_start: 0.5901 (mttt) cc_final: 0.4954 (mmpt) REVERT: D 717 ARG cc_start: 0.6234 (ttt180) cc_final: 0.5839 (ttp-170) REVERT: D 720 MET cc_start: 0.6417 (mmm) cc_final: 0.5498 (mmp) REVERT: D 727 CYS cc_start: 0.7465 (t) cc_final: 0.7051 (m) REVERT: D 852 ARG cc_start: 0.6725 (mpt-90) cc_final: 0.6294 (mmt90) REVERT: D 853 PHE cc_start: 0.7207 (m-80) cc_final: 0.6755 (m-80) REVERT: D 864 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.5108 (tp30) REVERT: D 868 LYS cc_start: 0.6313 (mttm) cc_final: 0.5916 (mtpm) REVERT: D 873 SER cc_start: 0.7051 (t) cc_final: 0.6768 (p) REVERT: D 930 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6263 (mm-30) REVERT: D 981 GLU cc_start: 0.7263 (tp30) cc_final: 0.6908 (tt0) REVERT: D 995 LEU cc_start: 0.7608 (mm) cc_final: 0.7349 (mm) REVERT: D 1004 ILE cc_start: 0.7319 (mp) cc_final: 0.6954 (mt) REVERT: D 1050 ARG cc_start: 0.6804 (ttm-80) cc_final: 0.6376 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6683 (ttmt) cc_final: 0.6377 (ttmm) outliers start: 25 outliers final: 14 residues processed: 461 average time/residue: 2.1640 time to fit residues: 1158.8867 Evaluate side-chains 458 residues out of total 2008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 436 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 851 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.150442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.121878 restraints weight = 57147.559| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.87 r_work: 0.3099 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18244 Z= 0.226 Angle : 0.530 8.926 24712 Z= 0.269 Chirality : 0.036 0.157 2888 Planarity : 0.004 0.078 3020 Dihedral : 4.785 57.576 2376 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.29 % Allowed : 22.62 % Favored : 76.08 % 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: 1.40 (0.18), residues: 2188 helix: 1.34 (0.13), residues: 1648 sheet: -1.33 (0.70), residues: 48 loop : -0.01 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 809 HIS 0.005 0.001 HIS D 700 PHE 0.012 0.001 PHE D 877 TYR 0.028 0.001 TYR B 842 ARG 0.014 0.000 ARG C 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17634.38 seconds wall clock time: 308 minutes 0.39 seconds (18480.39 seconds total)