Starting phenix.real_space_refine on Fri Feb 23 02:08:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj5_21688/02_2024/6wj5_21688_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj5_21688/02_2024/6wj5_21688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj5_21688/02_2024/6wj5_21688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj5_21688/02_2024/6wj5_21688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj5_21688/02_2024/6wj5_21688_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj5_21688/02_2024/6wj5_21688_trim_updated.pdb" } resolution = 3.6 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= 0.007 sd= 0.036 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: 6 Type Number sf(0) Gaussians S 144 5.16 5 C 11812 2.51 5 N 2972 2.21 5 O 3092 1.98 5 F 32 1.80 5 H 18268 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 GLU 632": "OE1" <-> "OE2" Residue "A PHE 640": "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 TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 909": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 922": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 999": "OD1" <-> "OD2" Residue "A TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 632": "OE1" <-> "OE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 785": "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 PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 864": "OE1" <-> "OE2" 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 898": "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 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1041": "OE1" <-> "OE2" 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 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 ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 854": "OE1" <-> "OE2" 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 909": "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 PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 947": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 1059": "OE1" <-> "OE2" 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 GLU 632": "OE1" <-> "OE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 854": "OE1" <-> "OE2" Residue "D PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 36320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} 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: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} 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: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} 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: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.33, per 1000 atoms: 0.45 Number of scatterers: 36320 At special positions: 0 Unit cell: (109.935, 108.888, 146.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 F 32 9.00 O 3092 8.00 N 2972 7.00 C 11812 6.00 H 18268 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: 31.58 Conformation dependent library (CDL) restraints added in 3.5 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 4 sheets defined 65.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.14 Creating SS restraints... Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 459 through 465 removed outlier: 3.707A pdb=" N ARG A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.714A pdb=" N GLN A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 527 through 540 removed outlier: 8.590A pdb=" N LYS A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.716A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 601 Processing helix chain 'A' and resid 605 through 610 removed outlier: 4.773A pdb=" N LYS A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 629 removed outlier: 3.985A pdb=" N GLU A 628 " --> pdb=" O THR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 641 removed outlier: 3.990A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.891A 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: 4.412A 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 removed outlier: 3.520A pdb=" N CYS A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.889A pdb=" N TRP A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.665A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 4.027A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 884 " --> pdb=" O LEU A 880 " (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: 3.941A pdb=" N MET A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 4.773A 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 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 987 removed outlier: 3.918A pdb=" N ASP A 966 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 4.409A 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: 3.549A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A1064 " --> pdb=" O LYS A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 459 through 465 removed outlier: 4.467A pdb=" N ARG B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.586A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 527 through 537 Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.726A pdb=" N ASN B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 605 through 610 removed outlier: 4.827A pdb=" N LYS B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 629 removed outlier: 3.771A pdb=" N GLU B 628 " --> pdb=" O THR B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 641 removed outlier: 3.761A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 3.846A 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: 4.509A 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 removed outlier: 3.555A pdb=" N CYS B 786 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 815 removed outlier: 3.881A pdb=" N TRP B 809 " --> pdb=" O ASN B 805 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 814 " --> pdb=" O ILE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 828 through 844 removed outlier: 3.634A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 852 removed outlier: 3.546A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 847 through 852' Processing helix chain 'B' and resid 854 through 891 removed outlier: 4.718A pdb=" N ILE B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 883 " --> pdb=" O PHE B 879 " (cutoff:3.500A) removed outlier: 3.503A 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: 4.819A 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 removed outlier: 3.507A pdb=" N ALA B 939 " --> pdb=" O VAL B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 989 removed outlier: 3.703A pdb=" N ILE B 957 " --> pdb=" O MET B 953 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 966 " --> pdb=" O GLY B 962 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 969 " --> pdb=" O ALA B 965 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 4.467A 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: 5.451A pdb=" N LEU B1045 " --> pdb=" O GLU B1041 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B1057 " --> pdb=" O ASP B1053 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B1063 " --> pdb=" O GLU B1059 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B1064 " --> pdb=" O LYS B1060 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B1067 " --> pdb=" O GLU B1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 455 Processing helix chain 'C' and resid 459 through 465 removed outlier: 4.530A 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 504 Processing helix chain 'C' and resid 517 through 523 Processing helix chain 'C' and resid 527 through 535 removed outlier: 4.040A pdb=" N ASP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) 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 557 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.769A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 601 Processing helix chain 'C' and resid 605 through 610 removed outlier: 4.800A pdb=" N LYS C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 removed outlier: 3.827A pdb=" N GLU C 628 " --> pdb=" O THR C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 641 removed outlier: 3.942A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 removed outlier: 3.529A pdb=" N ALA C 688 " --> pdb=" O THR C 684 " (cutoff:3.500A) 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: 3.626A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.517A 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 removed outlier: 4.160A pdb=" N CYS C 786 " --> pdb=" O ILE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 815 removed outlier: 4.128A pdb=" N TRP C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 814 " --> pdb=" O ILE C 810 " (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 852 removed outlier: 3.689A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 3.533A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 3.662A 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 910 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 967 removed outlier: 3.757A pdb=" N ASP C 966 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 989 removed outlier: 4.352A 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: 5.393A pdb=" N LEU C1045 " --> pdb=" O GLU C1041 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C1063 " --> pdb=" O GLU C1059 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C1064 " --> pdb=" O LYS C1060 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C1067 " --> pdb=" O GLU C1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 455 Processing helix chain 'D' and resid 459 through 465 removed outlier: 4.413A pdb=" N ARG D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 517 through 523 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.939A pdb=" N THR D 541 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.847A 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 557 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.748A pdb=" N ASN D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 605 through 610 removed outlier: 4.825A pdb=" N LYS D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 629 removed outlier: 3.967A pdb=" N GLU D 628 " --> pdb=" O THR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 641 removed outlier: 3.945A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.547A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.398A 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 removed outlier: 3.693A pdb=" N CYS D 786 " --> pdb=" O ILE D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 815 removed outlier: 3.918A pdb=" N TRP D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 814 " --> pdb=" O ILE D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 822 No H-bonds generated for 'chain 'D' and resid 820 through 822' Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.711A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 891 removed outlier: 3.641A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.920A pdb=" N MET D 912 " --> pdb=" O THR D 908 " (cutoff:3.500A) removed outlier: 4.787A 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 removed outlier: 3.501A pdb=" N ARG D 928 " --> pdb=" O GLU D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 934 through 947 removed outlier: 3.600A pdb=" N SER D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 989 removed outlier: 3.768A pdb=" N ASP D 966 " --> pdb=" O GLY D 962 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 969 " --> pdb=" O ALA D 965 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D 970 " --> pdb=" O ASP D 966 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 4.467A 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: 5.457A pdb=" N LEU D1045 " --> pdb=" O GLU D1041 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D1063 " --> pdb=" O GLU D1059 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D1064 " --> pdb=" O LYS D1060 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= C, first strand: chain 'C' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'D' and resid 642 through 644 861 hydrogen bonds defined for protein. 2571 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: 14.32 Time building geometry restraints manager: 32.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 18216 1.13 - 1.30: 2900 1.30 - 1.48: 7116 1.48 - 1.65: 8260 1.65 - 1.82: 228 Bond restraints: 36720 Sorted by residual: bond pdb=" N HIS B 983 " pdb=" H HIS B 983 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LEU C 466 " pdb=" H LEU C 466 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE C 783 " pdb=" H PHE C 783 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN B 917 " pdb=" H ASN B 917 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE D 905 " pdb=" H ILE D 905 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 36715 not shown) Histogram of bond angle deviations from ideal: 94.81 - 102.80: 212 102.80 - 110.79: 37478 110.79 - 118.78: 13440 118.78 - 126.77: 15090 126.77 - 134.76: 292 Bond angle restraints: 66512 Sorted by residual: angle pdb=" CA ASP B 511 " pdb=" CB ASP B 511 " pdb=" CG ASP B 511 " ideal model delta sigma weight residual 112.60 120.40 -7.80 1.00e+00 1.00e+00 6.09e+01 angle pdb=" CA ASP C 511 " pdb=" CB ASP C 511 " pdb=" CG ASP C 511 " ideal model delta sigma weight residual 112.60 120.03 -7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" CA ASP A 511 " pdb=" CB ASP A 511 " pdb=" CG ASP A 511 " ideal model delta sigma weight residual 112.60 120.01 -7.41 1.00e+00 1.00e+00 5.50e+01 angle pdb=" CA ASN D 577 " pdb=" CB ASN D 577 " pdb=" CG ASN D 577 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP D 511 " pdb=" CB ASP D 511 " pdb=" CG ASP D 511 " ideal model delta sigma weight residual 112.60 119.03 -6.43 1.00e+00 1.00e+00 4.13e+01 ... (remaining 66507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 15819 17.87 - 35.74: 903 35.74 - 53.60: 238 53.60 - 71.47: 235 71.47 - 89.34: 21 Dihedral angle restraints: 17216 sinusoidal: 9264 harmonic: 7952 Sorted by residual: 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 -136.22 14.22 0 2.50e+00 1.60e-01 3.24e+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 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASP A 763 " pdb=" C ASP A 763 " pdb=" N THR A 764 " pdb=" CA THR A 764 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 17213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2066 0.098 - 0.197: 736 0.197 - 0.295: 117 0.295 - 0.393: 13 0.393 - 0.491: 4 Chirality restraints: 2936 Sorted by residual: chirality pdb=" CA VAL C 948 " pdb=" N VAL C 948 " pdb=" C VAL C 948 " pdb=" CB VAL C 948 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA VAL A 948 " pdb=" N VAL A 948 " pdb=" C VAL A 948 " pdb=" CB VAL A 948 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.34e+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 2.02 0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 2933 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 458 " 0.324 9.50e-02 1.11e+02 1.56e-01 2.97e+02 pdb=" NE ARG B 458 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 458 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG B 458 " -0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG B 458 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 458 " -0.078 2.00e-02 2.50e+03 pdb="HH12 ARG B 458 " 0.233 2.00e-02 2.50e+03 pdb="HH21 ARG B 458 " 0.121 2.00e-02 2.50e+03 pdb="HH22 ARG B 458 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 458 " -0.328 9.50e-02 1.11e+02 1.53e-01 2.72e+02 pdb=" NE ARG D 458 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG D 458 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG D 458 " 0.081 2.00e-02 2.50e+03 pdb=" NH2 ARG D 458 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG D 458 " 0.083 2.00e-02 2.50e+03 pdb="HH12 ARG D 458 " -0.228 2.00e-02 2.50e+03 pdb="HH21 ARG D 458 " -0.097 2.00e-02 2.50e+03 pdb="HH22 ARG D 458 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 458 " 0.318 9.50e-02 1.11e+02 1.48e-01 2.51e+02 pdb=" NE ARG C 458 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 458 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG C 458 " -0.083 2.00e-02 2.50e+03 pdb=" NH2 ARG C 458 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 458 " -0.050 2.00e-02 2.50e+03 pdb="HH12 ARG C 458 " 0.208 2.00e-02 2.50e+03 pdb="HH21 ARG C 458 " 0.121 2.00e-02 2.50e+03 pdb="HH22 ARG C 458 " -0.165 2.00e-02 2.50e+03 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 2519 2.23 - 2.82: 71340 2.82 - 3.41: 103927 3.41 - 4.01: 134774 4.01 - 4.60: 198254 Nonbonded interactions: 510814 Sorted by model distance: nonbonded pdb=" OE1 GLU D 808 " pdb=" HH TYR D 812 " model vdw 1.632 1.850 nonbonded pdb=" HB3 SER C 921 " pdb="HH12 ARG D 919 " model vdw 1.635 2.270 nonbonded pdb=" OE1 GLN D 664 " pdb=" HH TYR D 706 " model vdw 1.647 1.850 nonbonded pdb=" OE1 GLU A 808 " pdb=" HH TYR A 812 " model vdw 1.651 1.850 nonbonded pdb=" OE1 GLU B 808 " pdb=" HH TYR B 812 " model vdw 1.656 1.850 ... (remaining 510809 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 group one per residue 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: 1.380 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: 0.540 Extract box with map and model: 7.950 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 115.840 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.012 0.085 18452 Z= 0.775 Angle : 1.838 10.741 25028 Z= 1.233 Chirality : 0.097 0.491 2936 Planarity : 0.014 0.142 3044 Dihedral : 13.447 89.341 6720 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.85 % Favored : 95.65 % Rotamer: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % 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: -2.50 (0.16), residues: 2208 helix: -2.01 (0.10), residues: 1620 sheet: 0.93 (0.66), residues: 60 loop : 0.08 (0.31), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.016 TRP C 993 HIS 0.017 0.005 HIS D 553 PHE 0.061 0.011 PHE C 898 TYR 0.189 0.025 TYR D 785 ARG 0.009 0.001 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 597 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 596 time to evaluate : 2.768 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: 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 509 LEU cc_start: 0.8363 (mt) cc_final: 0.8159 (mt) REVERT: A 603 LYS cc_start: 0.9320 (mttt) cc_final: 0.9059 (pttt) REVERT: A 705 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 720 MET cc_start: 0.7784 (mmm) cc_final: 0.7265 (mmt) REVERT: A 721 MET cc_start: 0.7016 (ttm) cc_final: 0.6760 (ttt) REVERT: A 774 MET cc_start: 0.8333 (mtm) cc_final: 0.7804 (mtp) REVERT: A 825 GLU cc_start: 0.8278 (tt0) cc_final: 0.7756 (pm20) REVERT: A 904 SER cc_start: 0.9357 (t) cc_final: 0.9111 (t) REVERT: A 915 ASP cc_start: 0.7627 (t0) cc_final: 0.7262 (p0) REVERT: A 969 LYS cc_start: 0.8818 (tttt) cc_final: 0.8378 (ttmt) REVERT: A 978 MET cc_start: 0.8382 (mtm) cc_final: 0.8111 (mtp) REVERT: A 1042 MET cc_start: 0.7685 (ppp) cc_final: 0.7120 (tmm) REVERT: A 1073 GLU cc_start: 0.8233 (tt0) cc_final: 0.7679 (tt0) REVERT: B 640 PHE cc_start: 0.8169 (m-80) cc_final: 0.7740 (m-10) REVERT: B 705 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6879 (mm-30) REVERT: B 717 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6914 (ttm170) REVERT: B 720 MET cc_start: 0.7894 (mmm) cc_final: 0.7443 (mmt) REVERT: B 721 MET cc_start: 0.7053 (ttm) cc_final: 0.6830 (ttt) REVERT: B 825 GLU cc_start: 0.8150 (tt0) cc_final: 0.7620 (pm20) REVERT: B 904 SER cc_start: 0.9330 (t) cc_final: 0.9090 (t) REVERT: B 915 ASP cc_start: 0.7851 (t0) cc_final: 0.7570 (p0) REVERT: B 996 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7994 (ttm110) REVERT: B 1042 MET cc_start: 0.7675 (ppp) cc_final: 0.6536 (tmm) REVERT: B 1046 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6739 (ttmt) REVERT: B 1056 PHE cc_start: 0.7900 (t80) cc_final: 0.7683 (t80) REVERT: B 1073 GLU cc_start: 0.8253 (tt0) cc_final: 0.7499 (tt0) REVERT: C 591 LYS cc_start: 0.8788 (mttt) cc_final: 0.8432 (mttp) REVERT: C 628 GLU cc_start: 0.8408 (tt0) cc_final: 0.8185 (tm-30) REVERT: C 705 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 720 MET cc_start: 0.7993 (mmm) cc_final: 0.7599 (mmt) REVERT: C 721 MET cc_start: 0.7012 (ttm) cc_final: 0.6767 (ttt) REVERT: C 825 GLU cc_start: 0.8331 (tt0) cc_final: 0.7747 (pm20) REVERT: C 904 SER cc_start: 0.9350 (t) cc_final: 0.9146 (t) REVERT: C 915 ASP cc_start: 0.7743 (t0) cc_final: 0.7432 (t0) REVERT: C 1042 MET cc_start: 0.7827 (ppp) cc_final: 0.7061 (tmm) REVERT: C 1046 LYS cc_start: 0.6853 (ttmt) cc_final: 0.6611 (ttmt) REVERT: C 1059 GLU cc_start: 0.7510 (tp30) cc_final: 0.7032 (tt0) REVERT: C 1073 GLU cc_start: 0.8118 (tt0) cc_final: 0.7538 (tt0) REVERT: D 591 LYS cc_start: 0.8854 (mttt) cc_final: 0.8470 (mttp) REVERT: D 709 MET cc_start: 0.7972 (tmt) cc_final: 0.7710 (tmm) REVERT: D 720 MET cc_start: 0.7887 (mmm) cc_final: 0.7472 (mmt) REVERT: D 721 MET cc_start: 0.7058 (ttm) cc_final: 0.6846 (ttt) REVERT: D 744 MET cc_start: 0.8144 (mmp) cc_final: 0.7899 (mmt) REVERT: D 825 GLU cc_start: 0.8168 (tt0) cc_final: 0.7620 (pm20) REVERT: D 904 SER cc_start: 0.9394 (t) cc_final: 0.9156 (t) REVERT: D 978 MET cc_start: 0.8384 (mtm) cc_final: 0.8131 (mtp) REVERT: D 987 GLU cc_start: 0.7001 (tt0) cc_final: 0.6629 (tt0) REVERT: D 1042 MET cc_start: 0.7326 (ppp) cc_final: 0.7010 (tpp) REVERT: D 1073 GLU cc_start: 0.8184 (tt0) cc_final: 0.7854 (tt0) outliers start: 1 outliers final: 0 residues processed: 596 average time/residue: 0.6851 time to fit residues: 624.8167 Evaluate side-chains 359 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 512 HIS A 549 ASN A 766 ASN A 831 GLN B 492 ASN B 512 HIS B 831 GLN C 476 ASN C 492 ASN C 512 HIS ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 831 GLN C 917 ASN C 940 GLN C1047 GLN D 512 HIS D 831 GLN D 940 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18452 Z= 0.210 Angle : 0.614 7.449 25028 Z= 0.321 Chirality : 0.040 0.165 2936 Planarity : 0.005 0.051 3044 Dihedral : 6.382 54.418 2496 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.92 % Allowed : 8.84 % Favored : 90.24 % 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: -0.71 (0.18), residues: 2208 helix: -0.49 (0.12), residues: 1608 sheet: -0.02 (0.70), residues: 68 loop : 0.16 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 832 HIS 0.006 0.001 HIS A 494 PHE 0.014 0.001 PHE B 823 TYR 0.020 0.002 TYR D 785 ARG 0.006 0.001 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 385 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 367 time to evaluate : 2.963 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: A 523 MET cc_start: 0.8779 (tpt) cc_final: 0.8366 (mmm) REVERT: A 558 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 603 LYS cc_start: 0.9260 (mttt) cc_final: 0.9032 (pttt) REVERT: A 660 PHE cc_start: 0.8340 (m-80) cc_final: 0.8037 (m-80) REVERT: A 705 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7164 (mm-30) REVERT: A 720 MET cc_start: 0.7552 (mmm) cc_final: 0.7203 (mmt) REVERT: A 721 MET cc_start: 0.6879 (ttm) cc_final: 0.6657 (ttt) REVERT: A 774 MET cc_start: 0.8127 (mtm) cc_final: 0.7853 (mtp) REVERT: A 825 GLU cc_start: 0.8106 (tt0) cc_final: 0.7702 (pm20) REVERT: A 852 ARG cc_start: 0.8097 (mpt180) cc_final: 0.7654 (mmt90) REVERT: A 915 ASP cc_start: 0.7888 (t0) cc_final: 0.7440 (p0) REVERT: A 1042 MET cc_start: 0.7580 (ppp) cc_final: 0.7103 (tmm) REVERT: B 825 GLU cc_start: 0.8019 (tt0) cc_final: 0.7565 (pm20) REVERT: B 915 ASP cc_start: 0.7860 (t0) cc_final: 0.7471 (p0) REVERT: B 987 GLU cc_start: 0.7309 (tt0) cc_final: 0.7020 (tt0) REVERT: B 1042 MET cc_start: 0.7747 (ppp) cc_final: 0.6777 (tmm) REVERT: B 1059 GLU cc_start: 0.7567 (tp30) cc_final: 0.6910 (mt-10) REVERT: C 628 GLU cc_start: 0.8393 (tt0) cc_final: 0.7963 (tm-30) REVERT: C 634 MET cc_start: 0.8550 (tpt) cc_final: 0.7788 (tpt) REVERT: C 720 MET cc_start: 0.7453 (mmm) cc_final: 0.7054 (mmt) REVERT: C 825 GLU cc_start: 0.8222 (tt0) cc_final: 0.7706 (pm20) REVERT: C 852 ARG cc_start: 0.8477 (mtt90) cc_final: 0.7528 (mtt180) REVERT: C 864 GLU cc_start: 0.7186 (tt0) cc_final: 0.6890 (mm-30) REVERT: C 987 GLU cc_start: 0.7275 (tt0) cc_final: 0.6980 (tt0) REVERT: C 1042 MET cc_start: 0.7832 (ppp) cc_final: 0.7032 (tmm) REVERT: C 1050 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.6941 (ttm110) REVERT: C 1059 GLU cc_start: 0.7475 (tp30) cc_final: 0.6761 (mt-10) REVERT: D 720 MET cc_start: 0.7578 (mmm) cc_final: 0.7305 (mmt) REVERT: D 721 MET cc_start: 0.6854 (ttm) cc_final: 0.6635 (ttt) REVERT: D 864 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6591 (mm-30) REVERT: D 987 GLU cc_start: 0.6901 (tt0) cc_final: 0.6486 (tt0) REVERT: D 1059 GLU cc_start: 0.7577 (tp30) cc_final: 0.6808 (mt-10) outliers start: 18 outliers final: 9 residues processed: 378 average time/residue: 0.6123 time to fit residues: 360.1468 Evaluate side-chains 308 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 299 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 875 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS B 940 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN C 917 ASN C1047 GLN D 537 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18452 Z= 0.399 Angle : 0.616 7.229 25028 Z= 0.331 Chirality : 0.040 0.202 2936 Planarity : 0.004 0.046 3044 Dihedral : 6.306 51.136 2496 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.48 % Allowed : 10.99 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2208 helix: -0.18 (0.13), residues: 1600 sheet: 0.01 (0.74), residues: 68 loop : 0.05 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 832 HIS 0.006 0.001 HIS D1062 PHE 0.017 0.002 PHE D 746 TYR 0.014 0.002 TYR B 840 ARG 0.008 0.001 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 325 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 3.040 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 558 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 603 LYS cc_start: 0.9284 (mttt) cc_final: 0.9044 (pttt) REVERT: A 623 ILE cc_start: 0.8271 (mm) cc_final: 0.7925 (mm) REVERT: A 625 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8312 (mm-30) REVERT: A 634 MET cc_start: 0.8542 (tpt) cc_final: 0.7855 (tpt) REVERT: A 660 PHE cc_start: 0.8586 (m-80) cc_final: 0.8234 (m-80) REVERT: A 705 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 720 MET cc_start: 0.7477 (mmm) cc_final: 0.6994 (mmt) REVERT: A 774 MET cc_start: 0.8256 (mtm) cc_final: 0.7884 (mtp) REVERT: A 825 GLU cc_start: 0.8211 (tt0) cc_final: 0.7710 (pm20) REVERT: A 852 ARG cc_start: 0.8089 (mpt180) cc_final: 0.7461 (mmt90) REVERT: A 915 ASP cc_start: 0.7805 (t0) cc_final: 0.7252 (p0) REVERT: A 969 LYS cc_start: 0.8694 (tttt) cc_final: 0.8358 (ttpt) REVERT: A 1042 MET cc_start: 0.7678 (ppp) cc_final: 0.6972 (tmm) REVERT: B 825 GLU cc_start: 0.8138 (tt0) cc_final: 0.7533 (pm20) REVERT: B 915 ASP cc_start: 0.7932 (t0) cc_final: 0.7517 (p0) REVERT: B 987 GLU cc_start: 0.7981 (tt0) cc_final: 0.7654 (tt0) REVERT: B 1042 MET cc_start: 0.7779 (ppp) cc_final: 0.6630 (tmm) REVERT: B 1059 GLU cc_start: 0.7601 (tp30) cc_final: 0.7222 (tp30) REVERT: C 591 LYS cc_start: 0.8987 (mttt) cc_final: 0.8590 (mtpp) REVERT: C 825 GLU cc_start: 0.8281 (tt0) cc_final: 0.7710 (pm20) REVERT: C 849 TYR cc_start: 0.7964 (m-80) cc_final: 0.7722 (m-10) REVERT: C 852 ARG cc_start: 0.8473 (mtt90) cc_final: 0.7564 (mtt180) REVERT: C 987 GLU cc_start: 0.7602 (tt0) cc_final: 0.7267 (tt0) REVERT: C 1042 MET cc_start: 0.7833 (ppp) cc_final: 0.6960 (tmm) REVERT: C 1059 GLU cc_start: 0.7543 (tp30) cc_final: 0.6812 (mt-10) REVERT: D 602 SER cc_start: 0.9155 (t) cc_final: 0.8919 (t) REVERT: D 774 MET cc_start: 0.8055 (mmm) cc_final: 0.7576 (mmm) REVERT: D 987 GLU cc_start: 0.7858 (tt0) cc_final: 0.7496 (tt0) REVERT: D 1050 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.7027 (ttm110) REVERT: D 1059 GLU cc_start: 0.7618 (tp30) cc_final: 0.6809 (mt-10) outliers start: 29 outliers final: 20 residues processed: 316 average time/residue: 0.6831 time to fit residues: 332.3678 Evaluate side-chains 293 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 273 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 136 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18452 Z= 0.191 Angle : 0.509 6.709 25028 Z= 0.265 Chirality : 0.037 0.156 2936 Planarity : 0.004 0.047 3044 Dihedral : 5.663 52.554 2496 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.23 % Allowed : 11.81 % Favored : 86.96 % 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 (0.18), residues: 2208 helix: 0.27 (0.13), residues: 1604 sheet: 0.58 (0.85), residues: 48 loop : 0.10 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 832 HIS 0.003 0.001 HIS B1062 PHE 0.008 0.001 PHE D 879 TYR 0.010 0.001 TYR B 840 ARG 0.007 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 316 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 292 time to evaluate : 2.838 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 603 LYS cc_start: 0.9247 (mttt) cc_final: 0.8981 (pttt) REVERT: A 625 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 785 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.6025 (m-10) REVERT: A 825 GLU cc_start: 0.8217 (tt0) cc_final: 0.7617 (pm20) REVERT: A 852 ARG cc_start: 0.8064 (mpt180) cc_final: 0.7458 (mmt90) REVERT: A 915 ASP cc_start: 0.7826 (t0) cc_final: 0.7258 (p0) REVERT: A 969 LYS cc_start: 0.8712 (tttt) cc_final: 0.8305 (ttmt) REVERT: A 978 MET cc_start: 0.8062 (mtp) cc_final: 0.7835 (mtp) REVERT: A 1042 MET cc_start: 0.7619 (ppp) cc_final: 0.6948 (tmm) REVERT: A 1050 ARG cc_start: 0.7311 (ttm-80) cc_final: 0.6796 (ttm110) REVERT: B 601 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8539 (mmm-85) REVERT: B 825 GLU cc_start: 0.8141 (tt0) cc_final: 0.7531 (pm20) REVERT: B 915 ASP cc_start: 0.7869 (t0) cc_final: 0.7417 (p0) REVERT: B 987 GLU cc_start: 0.7906 (tt0) cc_final: 0.7549 (tt0) REVERT: B 1042 MET cc_start: 0.7766 (ppp) cc_final: 0.6700 (tmm) REVERT: B 1059 GLU cc_start: 0.7576 (tp30) cc_final: 0.7022 (tp30) REVERT: C 825 GLU cc_start: 0.8261 (tt0) cc_final: 0.7651 (pm20) REVERT: C 852 ARG cc_start: 0.8352 (mtt90) cc_final: 0.7413 (mtt180) REVERT: C 987 GLU cc_start: 0.7759 (tt0) cc_final: 0.7425 (tt0) REVERT: C 1042 MET cc_start: 0.7853 (ppp) cc_final: 0.6938 (tmm) REVERT: C 1059 GLU cc_start: 0.7570 (tp30) cc_final: 0.6817 (mt-10) REVERT: D 602 SER cc_start: 0.9121 (t) cc_final: 0.8888 (t) REVERT: D 774 MET cc_start: 0.7943 (mmm) cc_final: 0.7423 (mmm) REVERT: D 987 GLU cc_start: 0.7181 (tt0) cc_final: 0.6807 (tt0) REVERT: D 1042 MET cc_start: 0.7562 (tpp) cc_final: 0.7084 (tpt) REVERT: D 1059 GLU cc_start: 0.7574 (tp30) cc_final: 0.6764 (mt-10) outliers start: 24 outliers final: 16 residues processed: 308 average time/residue: 0.6397 time to fit residues: 303.4689 Evaluate side-chains 292 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 275 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18452 Z= 0.232 Angle : 0.505 6.908 25028 Z= 0.264 Chirality : 0.037 0.141 2936 Planarity : 0.004 0.035 3044 Dihedral : 5.395 53.093 2496 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.28 % Allowed : 12.68 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2208 helix: 0.45 (0.13), residues: 1604 sheet: 0.76 (0.87), residues: 48 loop : 0.06 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 832 HIS 0.003 0.001 HIS B1062 PHE 0.010 0.001 PHE B 746 TYR 0.011 0.001 TYR D 726 ARG 0.005 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 321 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 296 time to evaluate : 2.786 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 535 ASP cc_start: 0.8107 (t0) cc_final: 0.7866 (t0) REVERT: A 603 LYS cc_start: 0.9233 (mttt) cc_final: 0.8954 (pttt) REVERT: A 625 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 785 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.5875 (m-10) REVERT: A 825 GLU cc_start: 0.8240 (tt0) cc_final: 0.7608 (pm20) REVERT: A 852 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7468 (mmt90) REVERT: A 915 ASP cc_start: 0.7813 (t0) cc_final: 0.7326 (p0) REVERT: A 969 LYS cc_start: 0.8698 (tttt) cc_final: 0.8311 (ttmt) REVERT: A 978 MET cc_start: 0.8032 (mtp) cc_final: 0.7789 (mtp) REVERT: A 1042 MET cc_start: 0.7622 (ppp) cc_final: 0.7048 (tmm) REVERT: A 1050 ARG cc_start: 0.7210 (ttm-80) cc_final: 0.6633 (ttm110) REVERT: B 601 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8680 (mmm-85) REVERT: B 774 MET cc_start: 0.8027 (mmm) cc_final: 0.7659 (mmm) REVERT: B 825 GLU cc_start: 0.8190 (tt0) cc_final: 0.7536 (pm20) REVERT: B 915 ASP cc_start: 0.7929 (t0) cc_final: 0.7517 (p0) REVERT: B 987 GLU cc_start: 0.7910 (tt0) cc_final: 0.7568 (tt0) REVERT: B 1042 MET cc_start: 0.7779 (ppp) cc_final: 0.6573 (tmm) REVERT: B 1059 GLU cc_start: 0.7594 (tp30) cc_final: 0.6820 (mt-10) REVERT: C 464 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7058 (ttp-170) REVERT: C 825 GLU cc_start: 0.8288 (tt0) cc_final: 0.7629 (pm20) REVERT: C 849 TYR cc_start: 0.7936 (m-80) cc_final: 0.7543 (m-10) REVERT: C 852 ARG cc_start: 0.8320 (mtt90) cc_final: 0.7391 (mtt180) REVERT: C 987 GLU cc_start: 0.7802 (tt0) cc_final: 0.7446 (tt0) REVERT: C 1042 MET cc_start: 0.7882 (ppp) cc_final: 0.6874 (tmm) REVERT: C 1059 GLU cc_start: 0.7552 (tp30) cc_final: 0.6819 (mt-10) REVERT: D 602 SER cc_start: 0.9108 (t) cc_final: 0.8867 (t) REVERT: D 774 MET cc_start: 0.7893 (mmm) cc_final: 0.7390 (mmm) REVERT: D 987 GLU cc_start: 0.7753 (tt0) cc_final: 0.7508 (tt0) REVERT: D 1059 GLU cc_start: 0.7547 (tp30) cc_final: 0.6758 (mt-10) outliers start: 25 outliers final: 21 residues processed: 313 average time/residue: 0.6163 time to fit residues: 300.4701 Evaluate side-chains 298 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 276 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18452 Z= 0.226 Angle : 0.493 6.683 25028 Z= 0.258 Chirality : 0.037 0.142 2936 Planarity : 0.003 0.035 3044 Dihedral : 5.274 53.577 2496 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.43 % Allowed : 13.50 % Favored : 85.07 % 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: 0.57 (0.18), residues: 2208 helix: 0.57 (0.13), residues: 1604 sheet: 0.98 (0.89), residues: 48 loop : 0.13 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 832 HIS 0.003 0.001 HIS B1062 PHE 0.010 0.001 PHE D 879 TYR 0.011 0.001 TYR B 840 ARG 0.004 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 321 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 293 time to evaluate : 2.765 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: A 535 ASP cc_start: 0.8140 (t0) cc_final: 0.7913 (t0) REVERT: A 603 LYS cc_start: 0.9222 (mttt) cc_final: 0.8942 (pttt) REVERT: A 625 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 785 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: A 825 GLU cc_start: 0.8216 (tt0) cc_final: 0.7592 (pm20) REVERT: A 852 ARG cc_start: 0.8110 (mpt180) cc_final: 0.7489 (mmt90) REVERT: A 915 ASP cc_start: 0.7754 (t0) cc_final: 0.7345 (p0) REVERT: A 969 LYS cc_start: 0.8688 (tttt) cc_final: 0.8361 (ttpt) REVERT: A 1042 MET cc_start: 0.7606 (ppp) cc_final: 0.7002 (tmm) REVERT: A 1050 ARG cc_start: 0.7282 (ttm-80) cc_final: 0.6752 (ttm110) REVERT: B 601 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8578 (mtp85) REVERT: B 735 ILE cc_start: 0.7904 (mm) cc_final: 0.7304 (mt) REVERT: B 825 GLU cc_start: 0.8188 (tt0) cc_final: 0.7541 (pm20) REVERT: B 915 ASP cc_start: 0.7917 (t0) cc_final: 0.7475 (p0) REVERT: B 987 GLU cc_start: 0.8048 (tt0) cc_final: 0.7734 (tt0) REVERT: B 1042 MET cc_start: 0.7715 (ppp) cc_final: 0.6538 (tmm) REVERT: B 1059 GLU cc_start: 0.7626 (tp30) cc_final: 0.6860 (mt-10) REVERT: C 464 ARG cc_start: 0.7685 (mtt-85) cc_final: 0.7064 (ttp-170) REVERT: C 825 GLU cc_start: 0.8307 (tt0) cc_final: 0.7601 (pm20) REVERT: C 852 ARG cc_start: 0.8275 (mtt90) cc_final: 0.7399 (mtt180) REVERT: C 987 GLU cc_start: 0.7952 (tt0) cc_final: 0.7610 (tt0) REVERT: C 1042 MET cc_start: 0.7811 (ppp) cc_final: 0.6862 (tmm) REVERT: C 1059 GLU cc_start: 0.7545 (tp30) cc_final: 0.6798 (mt-10) REVERT: D 602 SER cc_start: 0.9078 (t) cc_final: 0.8832 (t) REVERT: D 987 GLU cc_start: 0.7771 (tt0) cc_final: 0.7532 (tt0) REVERT: D 1059 GLU cc_start: 0.7653 (tp30) cc_final: 0.6894 (mt-10) outliers start: 28 outliers final: 23 residues processed: 311 average time/residue: 0.6356 time to fit residues: 306.5271 Evaluate side-chains 302 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18452 Z= 0.249 Angle : 0.499 6.833 25028 Z= 0.261 Chirality : 0.037 0.146 2936 Planarity : 0.003 0.035 3044 Dihedral : 5.217 53.749 2496 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.43 % Allowed : 13.50 % Favored : 85.07 % 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: 0.62 (0.18), residues: 2208 helix: 0.62 (0.13), residues: 1604 sheet: 1.03 (0.88), residues: 48 loop : 0.10 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 832 HIS 0.003 0.001 HIS B1062 PHE 0.010 0.001 PHE D 879 TYR 0.011 0.001 TYR B 840 ARG 0.004 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 310 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 282 time to evaluate : 2.854 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 536 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7627 (t) REVERT: A 603 LYS cc_start: 0.9224 (mttt) cc_final: 0.8941 (pttt) REVERT: A 625 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7894 (mm-30) REVERT: A 735 ILE cc_start: 0.7875 (mm) cc_final: 0.7273 (mt) REVERT: A 785 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5908 (m-10) REVERT: A 825 GLU cc_start: 0.8216 (tt0) cc_final: 0.7587 (pm20) REVERT: A 852 ARG cc_start: 0.8087 (mpt180) cc_final: 0.7447 (mmt90) REVERT: A 915 ASP cc_start: 0.7751 (t0) cc_final: 0.7426 (p0) REVERT: A 969 LYS cc_start: 0.8735 (tttt) cc_final: 0.8439 (ttpt) REVERT: A 1042 MET cc_start: 0.7540 (ppp) cc_final: 0.6957 (tmm) REVERT: A 1050 ARG cc_start: 0.7336 (ttm-80) cc_final: 0.6747 (ttm110) REVERT: B 735 ILE cc_start: 0.7912 (mm) cc_final: 0.7310 (mt) REVERT: B 774 MET cc_start: 0.8039 (mmm) cc_final: 0.7568 (mmm) REVERT: B 825 GLU cc_start: 0.8215 (tt0) cc_final: 0.7523 (pm20) REVERT: B 915 ASP cc_start: 0.7961 (t0) cc_final: 0.7484 (p0) REVERT: B 987 GLU cc_start: 0.8050 (tt0) cc_final: 0.7801 (tt0) REVERT: B 1042 MET cc_start: 0.7728 (ppp) cc_final: 0.6837 (tpp) REVERT: B 1059 GLU cc_start: 0.7621 (tp30) cc_final: 0.6852 (mt-10) REVERT: C 825 GLU cc_start: 0.8333 (tt0) cc_final: 0.7596 (pm20) REVERT: C 852 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7308 (mtt180) REVERT: C 987 GLU cc_start: 0.7982 (tt0) cc_final: 0.7638 (tt0) REVERT: C 1042 MET cc_start: 0.7823 (ppp) cc_final: 0.6898 (tpp) REVERT: C 1059 GLU cc_start: 0.7543 (tp30) cc_final: 0.6789 (mt-10) REVERT: D 602 SER cc_start: 0.9074 (t) cc_final: 0.8829 (t) REVERT: D 987 GLU cc_start: 0.7845 (tt0) cc_final: 0.7644 (tt0) REVERT: D 1059 GLU cc_start: 0.7635 (tp30) cc_final: 0.6901 (mt-10) outliers start: 28 outliers final: 22 residues processed: 301 average time/residue: 0.6506 time to fit residues: 309.1993 Evaluate side-chains 297 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 273 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 169 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18452 Z= 0.138 Angle : 0.464 6.406 25028 Z= 0.238 Chirality : 0.036 0.151 2936 Planarity : 0.004 0.072 3044 Dihedral : 4.955 56.404 2496 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.28 % Allowed : 13.65 % Favored : 85.07 % 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: 0.94 (0.18), residues: 2208 helix: 0.90 (0.13), residues: 1604 sheet: 1.32 (0.88), residues: 48 loop : 0.03 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 711 HIS 0.002 0.000 HIS A 494 PHE 0.008 0.001 PHE D 879 TYR 0.009 0.001 TYR D 726 ARG 0.014 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 333 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 308 time to evaluate : 2.754 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: A 475 LEU cc_start: 0.8234 (tp) cc_final: 0.8012 (tt) REVERT: A 603 LYS cc_start: 0.9183 (mttt) cc_final: 0.8904 (pttt) REVERT: A 625 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 735 ILE cc_start: 0.7837 (mm) cc_final: 0.7249 (mt) REVERT: A 785 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5614 (m-10) REVERT: A 825 GLU cc_start: 0.8208 (tt0) cc_final: 0.7565 (pm20) REVERT: A 852 ARG cc_start: 0.8085 (mpt180) cc_final: 0.7476 (mmt90) REVERT: A 915 ASP cc_start: 0.7720 (t0) cc_final: 0.7305 (p0) REVERT: A 969 LYS cc_start: 0.8687 (tttt) cc_final: 0.8382 (ttpt) REVERT: A 1042 MET cc_start: 0.7571 (ppp) cc_final: 0.6889 (tmm) REVERT: A 1050 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.6746 (ttm110) REVERT: B 601 ARG cc_start: 0.8873 (ttm110) cc_final: 0.8648 (mmm-85) REVERT: B 735 ILE cc_start: 0.7852 (mm) cc_final: 0.7274 (mt) REVERT: B 748 SER cc_start: 0.9187 (p) cc_final: 0.8810 (t) REVERT: B 825 GLU cc_start: 0.8168 (tt0) cc_final: 0.7525 (pm20) REVERT: B 915 ASP cc_start: 0.7900 (t0) cc_final: 0.7376 (p0) REVERT: B 987 GLU cc_start: 0.8056 (tt0) cc_final: 0.7788 (tt0) REVERT: B 1042 MET cc_start: 0.7645 (ppp) cc_final: 0.6593 (tpp) REVERT: B 1059 GLU cc_start: 0.7616 (tp30) cc_final: 0.6820 (mt-10) REVERT: C 464 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7087 (ttp-170) REVERT: C 825 GLU cc_start: 0.8306 (tt0) cc_final: 0.7631 (pm20) REVERT: C 852 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7252 (mtt180) REVERT: C 987 GLU cc_start: 0.7964 (tt0) cc_final: 0.7642 (tt0) REVERT: C 1042 MET cc_start: 0.7732 (ppp) cc_final: 0.6847 (tpp) REVERT: C 1059 GLU cc_start: 0.7541 (tp30) cc_final: 0.6746 (mt-10) REVERT: D 483 MET cc_start: 0.8141 (mtp) cc_final: 0.7024 (mmt) REVERT: D 602 SER cc_start: 0.9112 (t) cc_final: 0.8849 (t) REVERT: D 748 SER cc_start: 0.9086 (p) cc_final: 0.8694 (t) REVERT: D 774 MET cc_start: 0.8198 (mtm) cc_final: 0.7918 (mtp) REVERT: D 987 GLU cc_start: 0.7749 (tt0) cc_final: 0.7492 (tt0) REVERT: D 1059 GLU cc_start: 0.7627 (tp30) cc_final: 0.6864 (mt-10) outliers start: 25 outliers final: 20 residues processed: 323 average time/residue: 0.6082 time to fit residues: 306.1562 Evaluate side-chains 306 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 285 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.2980 chunk 206 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 ASN D 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18452 Z= 0.137 Angle : 0.466 6.607 25028 Z= 0.238 Chirality : 0.035 0.139 2936 Planarity : 0.003 0.053 3044 Dihedral : 4.762 56.799 2496 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.02 % Allowed : 14.42 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.19), residues: 2208 helix: 1.07 (0.13), residues: 1608 sheet: 1.47 (0.89), residues: 48 loop : -0.02 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 993 HIS 0.002 0.000 HIS D 589 PHE 0.008 0.001 PHE D 823 TYR 0.009 0.001 TYR D 726 ARG 0.011 0.000 ARG B 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 312 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 292 time to evaluate : 3.128 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 475 LEU cc_start: 0.8248 (tp) cc_final: 0.8039 (tt) REVERT: A 523 MET cc_start: 0.8519 (tpt) cc_final: 0.8040 (tmm) REVERT: A 603 LYS cc_start: 0.9161 (mttt) cc_final: 0.8897 (pttt) REVERT: A 625 GLU cc_start: 0.8626 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 735 ILE cc_start: 0.7808 (mm) cc_final: 0.7240 (mt) REVERT: A 785 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5434 (m-10) REVERT: A 825 GLU cc_start: 0.8190 (tt0) cc_final: 0.7542 (pm20) REVERT: A 852 ARG cc_start: 0.8089 (mpt180) cc_final: 0.7480 (mmt90) REVERT: A 915 ASP cc_start: 0.7755 (t0) cc_final: 0.7318 (p0) REVERT: A 969 LYS cc_start: 0.8731 (tttt) cc_final: 0.8426 (ttpt) REVERT: A 1042 MET cc_start: 0.7535 (ppp) cc_final: 0.6884 (tmm) REVERT: A 1050 ARG cc_start: 0.7277 (ttm-80) cc_final: 0.6749 (ttm110) REVERT: B 483 MET cc_start: 0.8110 (mtp) cc_final: 0.7500 (mmt) REVERT: B 601 ARG cc_start: 0.8873 (ttm110) cc_final: 0.8622 (mtp85) REVERT: B 735 ILE cc_start: 0.7706 (mm) cc_final: 0.7124 (mt) REVERT: B 748 SER cc_start: 0.9185 (p) cc_final: 0.8823 (t) REVERT: B 825 GLU cc_start: 0.8146 (tt0) cc_final: 0.7492 (pm20) REVERT: B 915 ASP cc_start: 0.7922 (t0) cc_final: 0.7355 (p0) REVERT: B 987 GLU cc_start: 0.8061 (tt0) cc_final: 0.7708 (tt0) REVERT: B 1042 MET cc_start: 0.7609 (ppp) cc_final: 0.6616 (tpp) REVERT: B 1059 GLU cc_start: 0.7596 (tp30) cc_final: 0.6797 (mt-10) REVERT: C 464 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7082 (ttp-170) REVERT: C 825 GLU cc_start: 0.8296 (tt0) cc_final: 0.7625 (pm20) REVERT: C 852 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7253 (mtt180) REVERT: C 987 GLU cc_start: 0.7954 (tt0) cc_final: 0.7630 (tt0) REVERT: C 1042 MET cc_start: 0.7695 (ppp) cc_final: 0.6829 (tpp) REVERT: C 1059 GLU cc_start: 0.7524 (tp30) cc_final: 0.6731 (mt-10) REVERT: D 483 MET cc_start: 0.8134 (mtp) cc_final: 0.7045 (mmt) REVERT: D 602 SER cc_start: 0.9081 (t) cc_final: 0.8818 (t) REVERT: D 748 SER cc_start: 0.9084 (p) cc_final: 0.8701 (t) REVERT: D 774 MET cc_start: 0.8214 (mtm) cc_final: 0.7891 (mtp) REVERT: D 987 GLU cc_start: 0.7713 (tt0) cc_final: 0.7434 (tt0) REVERT: D 1059 GLU cc_start: 0.7609 (tp30) cc_final: 0.6835 (mt-10) outliers start: 20 outliers final: 19 residues processed: 304 average time/residue: 0.6284 time to fit residues: 299.8265 Evaluate side-chains 305 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 285 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18452 Z= 0.256 Angle : 0.496 6.590 25028 Z= 0.258 Chirality : 0.037 0.141 2936 Planarity : 0.004 0.054 3044 Dihedral : 4.922 55.681 2496 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.12 % Allowed : 14.42 % Favored : 84.46 % 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: 0.98 (0.18), residues: 2208 helix: 0.95 (0.13), residues: 1604 sheet: 1.28 (0.87), residues: 48 loop : -0.04 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 832 HIS 0.004 0.001 HIS B1062 PHE 0.011 0.001 PHE D 879 TYR 0.011 0.001 TYR B 840 ARG 0.010 0.000 ARG B 601 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 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 305 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 283 time to evaluate : 2.786 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 536 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7637 (t) REVERT: A 603 LYS cc_start: 0.9171 (mttt) cc_final: 0.8901 (pttt) REVERT: A 625 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 735 ILE cc_start: 0.7875 (mm) cc_final: 0.7301 (mt) REVERT: A 785 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5562 (m-10) REVERT: A 825 GLU cc_start: 0.8206 (tt0) cc_final: 0.7532 (pm20) REVERT: A 852 ARG cc_start: 0.8127 (mpt180) cc_final: 0.7495 (mmt90) REVERT: A 915 ASP cc_start: 0.7627 (t0) cc_final: 0.7319 (p0) REVERT: A 969 LYS cc_start: 0.8705 (tttt) cc_final: 0.8385 (ttpt) REVERT: A 1042 MET cc_start: 0.7544 (ppp) cc_final: 0.6920 (tmm) REVERT: A 1050 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6802 (ttm110) REVERT: B 601 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8597 (mtp85) REVERT: B 735 ILE cc_start: 0.7756 (mm) cc_final: 0.7167 (mt) REVERT: B 748 SER cc_start: 0.9238 (p) cc_final: 0.8721 (t) REVERT: B 825 GLU cc_start: 0.8233 (tt0) cc_final: 0.7523 (pm20) REVERT: B 915 ASP cc_start: 0.7952 (t0) cc_final: 0.7495 (p0) REVERT: B 987 GLU cc_start: 0.8024 (tt0) cc_final: 0.7766 (tt0) REVERT: B 1042 MET cc_start: 0.7629 (ppp) cc_final: 0.6646 (tpp) REVERT: B 1059 GLU cc_start: 0.7613 (tp30) cc_final: 0.6808 (mt-10) REVERT: C 749 THR cc_start: 0.9194 (p) cc_final: 0.8918 (t) REVERT: C 825 GLU cc_start: 0.8273 (tt0) cc_final: 0.7577 (pm20) REVERT: C 852 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7311 (mtt180) REVERT: C 987 GLU cc_start: 0.8019 (tt0) cc_final: 0.7769 (tt0) REVERT: C 1042 MET cc_start: 0.7647 (ppp) cc_final: 0.6819 (tpp) REVERT: C 1059 GLU cc_start: 0.7483 (tp30) cc_final: 0.6712 (mt-10) REVERT: D 483 MET cc_start: 0.8229 (mtp) cc_final: 0.6904 (mmt) REVERT: D 602 SER cc_start: 0.9057 (t) cc_final: 0.8792 (t) REVERT: D 748 SER cc_start: 0.9158 (p) cc_final: 0.8802 (t) REVERT: D 774 MET cc_start: 0.8237 (mtm) cc_final: 0.7903 (mtp) REVERT: D 987 GLU cc_start: 0.7756 (tt0) cc_final: 0.7543 (tt0) REVERT: D 1059 GLU cc_start: 0.7653 (tp30) cc_final: 0.6908 (mt-10) outliers start: 22 outliers final: 19 residues processed: 297 average time/residue: 0.6181 time to fit residues: 288.7529 Evaluate side-chains 300 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 279 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.097758 restraints weight = 73238.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.102100 restraints weight = 29299.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104783 restraints weight = 16772.662| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18452 Z= 0.226 Angle : 0.493 6.749 25028 Z= 0.255 Chirality : 0.036 0.141 2936 Planarity : 0.003 0.051 3044 Dihedral : 4.942 55.530 2496 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.12 % Allowed : 14.31 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.18), residues: 2208 helix: 0.96 (0.13), residues: 1604 sheet: 1.35 (0.88), residues: 48 loop : -0.04 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 832 HIS 0.003 0.001 HIS B1062 PHE 0.011 0.001 PHE D 879 TYR 0.010 0.001 TYR B 840 ARG 0.010 0.000 ARG B 601 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7254.09 seconds wall clock time: 129 minutes 32.46 seconds (7772.46 seconds total)