Starting phenix.real_space_refine on Tue Feb 20 16:35:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9m_13873/02_2024/7q9m_13873.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9m_13873/02_2024/7q9m_13873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9m_13873/02_2024/7q9m_13873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9m_13873/02_2024/7q9m_13873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9m_13873/02_2024/7q9m_13873.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9m_13873/02_2024/7q9m_13873.pdb" } resolution = 3.7 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= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 125 5.16 5 C 18061 2.51 5 N 4676 2.21 5 O 5544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28406 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7473 Classifications: {'peptide': 976} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 34} Link IDs: {'PTRANS': 48, 'TRANS': 927} Chain breaks: 10 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 7596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7596 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 48, 'TRANS': 929} Chain breaks: 10 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7452 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 49, 'TRANS': 925} Chain breaks: 12 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 108 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "J" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "E" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.76, per 1000 atoms: 0.52 Number of scatterers: 28406 At special positions: 0 Unit cell: (131.2, 168.92, 205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 125 16.00 O 5544 8.00 N 4676 7.00 C 18061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.02 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 279 " " NAG A1302 " - " ASN A 328 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 706 " " NAG A1305 " - " ASN A1071 " " NAG B1301 " - " ASN B 714 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B 706 " " NAG B1306 " - " ASN B1071 " " NAG C1301 " - " ASN C 613 " " NAG C1302 " - " ASN C 654 " " NAG C1303 " - " ASN C 706 " " NAG C1304 " - " ASN C1071 " " NAG D 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN A 234 " " NAG O 1 " - " ASN B 340 " " NAG P 1 " - " ASN B 798 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 340 " " NAG S 1 " - " ASN C1131 " " NAG T 1 " - " ASN C 714 " " NAG U 1 " - " ASN C 798 " " NAG V 1 " - " ASN C1095 " Time building additional restraints: 11.60 Conformation dependent library (CDL) restraints added in 4.7 seconds 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6722 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 58 sheets defined 22.5% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.334A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.089A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.636A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.522A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.602A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.541A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 3.790A pdb=" N ALA A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.442A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.129A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 368 Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.272A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.150A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.523A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.522A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.134A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.269A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.981A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.013A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 753 removed outlier: 3.755A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 888 Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.562A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 Processing helix chain 'C' and resid 943 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.220A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.375A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.722A pdb=" N GLN H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.739A pdb=" N GLN J 65 " --> pdb=" O PRO J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.833A pdb=" N GLN E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.638A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 264 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 263 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 93 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.792A pdb=" N ASP A 53 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.505A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 316 removed outlier: 7.138A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 610 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 325 removed outlier: 5.600A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.579A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA8, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.233A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.669A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.569A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.294A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 30 removed outlier: 8.481A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.126A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.281A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 322 through 323 Processing sheet with id=AC1, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.762A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC4, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.063A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.852A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.560A pdb=" N ILE B 711 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B1070 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 715 through 725 removed outlier: 7.020A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.271A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.500A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.586A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.513A pdb=" N ASP C 53 " --> pdb=" O ARG C 270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.952A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 316 removed outlier: 6.888A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.693A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASN C 539 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.848A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.964A pdb=" N CYS C 522 " --> pdb=" O CYS C 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE1, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE2, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.550A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.601A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.601A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AE6, first strand: chain 'C' and resid 1117 through 1120 removed outlier: 3.730A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.667A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.539A pdb=" N HIS H 105 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.652A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.561A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.705A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.608A pdb=" N GLU K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.525A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.758A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.502A pdb=" N VAL F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.619A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3180 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: 13.76 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4979 1.33 - 1.45: 7984 1.45 - 1.57: 15921 1.57 - 1.69: 0 1.69 - 1.82: 158 Bond restraints: 29042 Sorted by residual: bond pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.66e+00 bond pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.62e+00 bond pdb=" N SER L 28 " pdb=" CA SER L 28 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.88e+00 bond pdb=" N ALA L 25 " pdb=" CA ALA L 25 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" N SER L 26 " pdb=" CA SER L 26 " ideal model delta sigma weight residual 1.462 1.488 -0.027 1.26e-02 6.30e+03 4.42e+00 ... (remaining 29037 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.64: 839 106.64 - 113.49: 16142 113.49 - 120.35: 10084 120.35 - 127.21: 12190 127.21 - 134.06: 302 Bond angle restraints: 39557 Sorted by residual: angle pdb=" CA SER L 26 " pdb=" C SER L 26 " pdb=" O SER L 26 " ideal model delta sigma weight residual 120.92 116.29 4.63 1.04e+00 9.25e-01 1.99e+01 angle pdb=" CA SER L 28 " pdb=" C SER L 28 " pdb=" O SER L 28 " ideal model delta sigma weight residual 121.87 118.22 3.65 1.16e+00 7.43e-01 9.91e+00 angle pdb=" N SER B 755 " pdb=" CA SER B 755 " pdb=" CB SER B 755 " ideal model delta sigma weight residual 114.27 109.55 4.72 1.64e+00 3.72e-01 8.29e+00 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.96 110.12 2.84 1.00e+00 1.00e+00 8.08e+00 angle pdb=" N GLN L 27 " pdb=" CA GLN L 27 " pdb=" CB GLN L 27 " ideal model delta sigma weight residual 110.49 115.29 -4.80 1.69e+00 3.50e-01 8.07e+00 ... (remaining 39552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 17160 21.64 - 43.28: 452 43.28 - 64.92: 90 64.92 - 86.57: 25 86.57 - 108.21: 9 Dihedral angle restraints: 17736 sinusoidal: 7276 harmonic: 10460 Sorted by residual: dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1040 " pdb=" CB CYS B1040 " ideal model delta sinusoidal sigma weight residual -86.00 -162.35 76.35 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -160.56 74.56 1 1.00e+01 1.00e-02 7.04e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -153.39 67.39 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 17733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4079 0.067 - 0.133: 524 0.133 - 0.200: 23 0.200 - 0.266: 1 0.266 - 0.333: 2 Chirality restraints: 4629 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.48e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.16e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 340 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4626 not shown) Planarity restraints: 5071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 994 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C ILE A 994 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE A 994 " -0.009 2.00e-02 2.50e+03 pdb=" N THR A 995 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 523 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 524 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 230 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.017 5.00e-02 4.00e+02 ... (remaining 5068 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 202 2.53 - 3.12: 22721 3.12 - 3.71: 42646 3.71 - 4.31: 61782 4.31 - 4.90: 103878 Nonbonded interactions: 231229 Sorted by model distance: nonbonded pdb=" O LYS F 108 " pdb=" CG ARG F 109 " model vdw 1.937 3.440 nonbonded pdb=" O PHE B 559 " pdb=" NZ LYS C 41 " model vdw 2.046 2.520 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.066 2.440 nonbonded pdb=" OG1 THR C 615 " pdb=" OE1 GLU C 616 " model vdw 2.071 2.440 nonbonded pdb=" OG SER E 31 " pdb=" OD2 ASP E 52 " model vdw 2.074 2.440 ... (remaining 231224 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' and (resid 27 through 87 or resid 90 through 96 or resid 100 through \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or re \ sid 141 through 240 or resid 261 through 328 or (resid 329 and (name N or name C \ A or name C or name O or name CB )) or resid 330 through 370 or (resid 371 and ( \ name N or name CA or name C or name O or name CB )) or resid 372 through 374 or \ (resid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 \ through 382 or (resid 383 and (name N or name CA or name C or name O or name CB \ )) or resid 384 through 452 or (resid 453 through 456 and (name N or name CA or \ name C or name O or name CB )) or resid 457 through 458 or (resid 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 461 or (res \ id 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 501 or (resid 502 and (name N or name CA or name C or name O or name CB )) \ or resid 503 through 525 or (resid 526 and (name N or name CA or name C or name \ O or name CB )) or resid 527 through 532 or (resid 533 through 534 and (name N o \ r name CA or name C or name O or name CB )) or resid 535 through 549 or (resid 5 \ 50 through 551 and (name N or name CA or name C or name O or name CB )) or resid \ 552 through 553 or (resid 554 through 555 and (name N or name CA or name C or n \ ame O or name CB )) or resid 556 or (resid 557 and (name N or name CA or name C \ or name O or name CB )) or resid 558 or (resid 559 and (name N or name CA or nam \ e C or name O or name CB )) or resid 560 through 570 or (resid 571 through 572 a \ nd (name N or name CA or name C or name O or name CB )) or resid 573 or (resid 5 \ 74 through 575 and (name N or name CA or name C or name O or name CB )) or resid \ 576 through 580 or (resid 581 and (name N or name CA or name C or name O or nam \ e CB )) or resid 582 through 672 or (resid 687 and (name N or name CA or name C \ or name O or name CB )) or resid 688 through 782 or (resid 783 and (name N or na \ me CA or name C or name O or name CB )) or resid 784 through 792 or (resid 793 a \ nd (name N or name CA or name C or name O or name CB )) or resid 794 through 821 \ or (resid 822 and (name N or name CA or name C or name O or name CB )) or resid \ 823 through 824 or resid 852 through 929 or (resid 930 and (name N or name CA o \ r name C or name O or name CB )) or resid 931 through 936 or resid 942 through 9 \ 79 or (resid 980 and (name N or name CA or name C or name O or name CB )) or res \ id 981 through 991 or (resid 992 and (name N or name CA or name C or name O or n \ ame CB )) or resid 993 through 1103 or (resid 1104 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1105 through 1144 or resid 1301 through 130 \ 4)) selection = (chain 'B' and (resid 27 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 through 65 or re \ sid 82 through 87 or resid 90 through 95 or (resid 96 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 101 or (resid 102 and (name \ N or name CA or name C or name O or name CB )) or resid 103 through 121 or resid \ 126 through 128 or (resid 129 and (name N or name CA or name C or name O or nam \ e CB )) or resid 130 through 139 or (resid 140 and (name N or name CA or name C \ or name O or name CB )) or resid 141 through 171 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 or (resid 202 through 203 and (name N or name CA or name C or name O or nam \ e CB )) or resid 204 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 232 or (resid 233 and (name N or na \ me CA or name C or name O )) or resid 234 or (resid 235 and (name N or name CA o \ r name C or name O or name CB )) or resid 236 through 277 or (resid 278 and (nam \ e N or name CA or name C or name O or name CB )) or resid 279 through 336 or (re \ sid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 th \ rough 342 or (resid 343 and (name N or name CA or name C or name O or name CB )) \ or resid 344 through 365 or (resid 366 and (name N or name CA or name C or name \ O or name CB )) or resid 367 through 370 or (resid 371 and (name N or name CA o \ r name C or name O or name CB )) or resid 372 through 373 or (resid 374 through \ 375 and (name N or name CA or name C or name O or name CB )) or resid 376 throug \ h 382 or (resid 383 and (name N or name CA or name C or name O or name CB )) or \ resid 384 or (resid 385 and (name N or name CA or name C or name O or name CB )) \ or (resid 389 and (name N or name CA or name C or name O or name CB )) or resid \ 390 through 452 or (resid 453 through 456 and (name N or name CA or name C or n \ ame O or name CB )) or resid 457 through 458 or (resid 459 and (name N or name C \ A or name C or name O or name CB )) or resid 460 through 461 or (resid 462 and ( \ name N or name CA or name C or name O or name CB )) or resid 463 through 470 or \ (resid 471 through 472 and (name N or name CA or name C or name O or name CB )) \ or resid 473 through 480 or (resid 481 and (name N or name CA or name C or name \ O or name CB )) or resid 482 through 497 or (resid 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 through 501 or (resid 502 and (name \ N or name CA or name C or name O or name CB )) or resid 503 through 525 or (res \ id 526 and (name N or name CA or name C or name O or name CB )) or resid 527 thr \ ough 532 or (resid 533 through 534 and (name N or name CA or name C or name O or \ name CB )) or resid 535 through 549 or (resid 550 through 551 and (name N or na \ me CA or name C or name O or name CB )) or resid 552 through 553 or (resid 554 t \ hrough 555 and (name N or name CA or name C or name O or name CB )) or resid 556 \ or (resid 557 and (name N or name CA or name C or name O or name CB )) or resid \ 558 or (resid 559 and (name N or name CA or name C or name O or name CB )) or r \ esid 560 through 570 or (resid 571 through 572 and (name N or name CA or name C \ or name O or name CB )) or resid 573 or (resid 574 through 575 and (name N or na \ me CA or name C or name O or name CB )) or resid 576 through 671 or (resid 672 a \ nd (name N or name CA or name C or name O or name CB )) or resid 687 through 821 \ or (resid 822 and (name N or name CA or name C or name O or name CB )) or resid \ 823 through 824 or resid 852 through 929 or (resid 930 and (name N or name CA o \ r name C or name O or name CB )) or resid 931 through 936 or resid 942 through 9 \ 79 or (resid 980 and (name N or name CA or name C or name O or name CB )) or res \ id 981 or (resid 982 and (name N or name CA or name C or name O or name CB )) or \ resid 983 through 984 or (resid 985 through 987 and (name N or name CA or name \ C or name O or name CB )) or resid 988 through 991 or (resid 992 and (name N or \ name CA or name C or name O or name CB )) or resid 993 through 1141 or (resid 11 \ 42 and (name N or name CA or name C or name O or name CB )) or resid 1143 throug \ h 1144 or resid 1301 through 1304)) selection = (chain 'C' and (resid 27 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 39 or (resid 40 and (name N or nam \ e CA or name C or name O or name CB )) or resid 41 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 through 65 or re \ sid 82 through 95 or (resid 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 100 through 128 or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or resid 130 through 171 or (resid 187 and (name N or na \ me CA or name C or name O or name CB )) or resid 188 through 194 or (resid 195 a \ nd (name N or name CA or name C or name O or name CB )) or resid 196 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 or (resid 202 through 203 and (name N or name CA or name C or name O or nam \ e CB )) or resid 204 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 225 or (resid 226 and (name N or na \ me CA or name C or name O or name CB )) or resid 227 through 232 or (resid 233 a \ nd (name N or name CA or name C or name O )) or resid 234 or (resid 235 and (nam \ e N or name CA or name C or name O or name CB )) or resid 236 or (resid 237 and \ (name N or name CA or name C or name O or name CB )) or resid 238 through 240 or \ resid 261 through 328 or (resid 329 and (name N or name CA or name C or name O \ or name CB )) or resid 330 through 384 or (resid 385 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 389 and (name N or name CA or name C or \ name O or name CB )) or resid 390 through 497 or (resid 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 through 513 or resid 521 throu \ gh 574 or (resid 575 and (name N or name CA or name C or name O or name CB )) or \ resid 576 through 579 or (resid 580 through 581 and (name N or name CA or name \ C or name O or name CB )) or resid 582 through 782 or (resid 783 and (name N or \ name CA or name C or name O or name CB )) or resid 784 through 792 or (resid 793 \ and (name N or name CA or name C or name O or name CB )) or resid 794 through 9 \ 81 or (resid 982 and (name N or name CA or name C or name O or name CB )) or res \ id 983 through 984 or (resid 985 through 987 and (name N or name CA or name C or \ name O or name CB )) or resid 988 through 1103 or (resid 1104 and (name N or na \ me CA or name C or name O or name CB )) or resid 1105 through 1141 or (resid 114 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 1143 through \ 1144 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = (chain 'E' and (resid 2 through 102 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 120)) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 19.260 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 77.720 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.004 0.052 29042 Z= 0.270 Angle : 0.565 6.149 39557 Z= 0.309 Chirality : 0.044 0.333 4629 Planarity : 0.003 0.031 5043 Dihedral : 10.543 108.208 10885 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.95 % Favored : 96.91 % Rotamer: Outliers : 0.75 % Allowed : 2.78 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.25 (0.14), residues: 3531 helix: 2.11 (0.20), residues: 666 sheet: -0.01 (0.17), residues: 918 loop : -0.39 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1099 HIS 0.005 0.001 HIS A1061 PHE 0.012 0.001 PHE B 799 TYR 0.017 0.001 TYR A1064 ARG 0.003 0.000 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 550 time to evaluate : 3.453 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: A 224 GLU cc_start: 0.8747 (pm20) cc_final: 0.8480 (pm20) REVERT: A 272 PHE cc_start: 0.8781 (m-80) cc_final: 0.8111 (m-80) REVERT: A 393 TYR cc_start: 0.8849 (m-80) cc_final: 0.8435 (m-10) REVERT: A 579 LEU cc_start: 0.8648 (mt) cc_final: 0.8382 (pt) REVERT: A 581 ILE cc_start: 0.8404 (mm) cc_final: 0.7682 (tt) REVERT: A 866 MET cc_start: 0.8456 (mtt) cc_final: 0.8123 (mtt) REVERT: B 129 LYS cc_start: 0.8252 (mttt) cc_final: 0.7780 (mmmt) REVERT: B 284 ASP cc_start: 0.8452 (t0) cc_final: 0.8247 (t0) REVERT: B 335 PHE cc_start: 0.8197 (m-80) cc_final: 0.7554 (m-80) REVERT: B 433 TRP cc_start: 0.7228 (p90) cc_final: 0.6961 (p90) REVERT: B 855 LEU cc_start: 0.8121 (mp) cc_final: 0.7841 (mp) REVERT: B 1026 MET cc_start: 0.9062 (tpp) cc_final: 0.8843 (tpp) REVERT: C 32 PHE cc_start: 0.8992 (m-80) cc_final: 0.8703 (m-10) REVERT: C 262 TYR cc_start: 0.6519 (p90) cc_final: 0.6209 (p90) REVERT: C 399 ILE cc_start: 0.7940 (pt) cc_final: 0.7603 (pt) REVERT: C 433 TRP cc_start: 0.8189 (p90) cc_final: 0.7718 (p90) REVERT: C 446 TYR cc_start: 0.8920 (m-80) cc_final: 0.8718 (m-80) REVERT: C 581 ILE cc_start: 0.8531 (mm) cc_final: 0.7886 (mm) REVERT: C 737 MET cc_start: 0.7739 (ttm) cc_final: 0.7539 (mtp) REVERT: C 1001 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9342 (tt) REVERT: H 34 ILE cc_start: 0.8134 (tt) cc_final: 0.7770 (tp) REVERT: H 80 TYR cc_start: 0.8969 (m-80) cc_final: 0.8659 (m-80) REVERT: L 36 TYR cc_start: 0.7286 (m-80) cc_final: 0.6995 (m-80) REVERT: L 49 TYR cc_start: 0.7994 (p90) cc_final: 0.7784 (p90) REVERT: J 98 ARG cc_start: 0.8191 (ttm170) cc_final: 0.7224 (ttp-170) REVERT: J 109 ASP cc_start: 0.7668 (p0) cc_final: 0.6905 (p0) REVERT: K 4 MET cc_start: 0.9117 (mmm) cc_final: 0.8701 (mmm) REVERT: K 54 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7628 (tmm-80) REVERT: E 95 TYR cc_start: 0.7237 (m-80) cc_final: 0.6760 (m-80) outliers start: 23 outliers final: 4 residues processed: 568 average time/residue: 0.4077 time to fit residues: 361.1883 Evaluate side-chains 323 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 318 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain E residue 33 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 277 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 168 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 321 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 196 ASN A 932 GLN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN C 447 ASN C 652 HIS C 911 ASN C1085 HIS ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN K 27 GLN E 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29042 Z= 0.278 Angle : 0.604 9.342 39557 Z= 0.306 Chirality : 0.045 0.214 4629 Planarity : 0.004 0.046 5043 Dihedral : 7.045 66.846 4759 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 2.16 % Allowed : 8.97 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.35 (0.14), residues: 3531 helix: 2.16 (0.20), residues: 673 sheet: 0.16 (0.17), residues: 889 loop : -0.38 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 104 HIS 0.008 0.001 HIS J 99 PHE 0.022 0.002 PHE A 92 TYR 0.034 0.002 TYR H 60 ARG 0.006 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 344 time to evaluate : 3.291 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: A 104 TRP cc_start: 0.7961 (m-90) cc_final: 0.7592 (m-90) REVERT: A 135 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5633 (p90) REVERT: A 224 GLU cc_start: 0.8733 (pm20) cc_final: 0.8490 (pm20) REVERT: A 272 PHE cc_start: 0.8675 (m-80) cc_final: 0.8324 (m-80) REVERT: A 335 PHE cc_start: 0.9099 (m-10) cc_final: 0.8869 (m-10) REVERT: A 449 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9175 (tt) REVERT: A 494 PHE cc_start: 0.8060 (m-80) cc_final: 0.7550 (m-80) REVERT: A 579 LEU cc_start: 0.8661 (mt) cc_final: 0.8361 (pt) REVERT: A 581 ILE cc_start: 0.8433 (mm) cc_final: 0.7742 (tt) REVERT: A 866 MET cc_start: 0.8417 (mtt) cc_final: 0.8116 (mtt) REVERT: A 952 ASN cc_start: 0.7836 (t0) cc_final: 0.7452 (t0) REVERT: B 295 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: B 335 PHE cc_start: 0.8032 (m-80) cc_final: 0.7687 (m-80) REVERT: B 433 TRP cc_start: 0.7221 (p90) cc_final: 0.6873 (p90) REVERT: B 987 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8531 (tm-30) REVERT: B 1080 HIS cc_start: 0.7880 (t70) cc_final: 0.7589 (t70) REVERT: C 230 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.8056 (Cg_endo) REVERT: C 266 TYR cc_start: 0.7390 (m-80) cc_final: 0.7059 (m-80) REVERT: C 367 ASN cc_start: 0.8699 (m-40) cc_final: 0.8278 (p0) REVERT: C 399 ILE cc_start: 0.8006 (pt) cc_final: 0.7619 (pt) REVERT: C 433 TRP cc_start: 0.8294 (p90) cc_final: 0.7786 (p90) REVERT: C 446 TYR cc_start: 0.8931 (m-80) cc_final: 0.8696 (m-10) REVERT: C 581 ILE cc_start: 0.8471 (mm) cc_final: 0.7882 (mm) REVERT: C 801 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6850 (mt0) REVERT: C 855 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8734 (mt) REVERT: C 1001 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9287 (tt) REVERT: L 49 TYR cc_start: 0.8184 (p90) cc_final: 0.7797 (p90) REVERT: L 79 GLN cc_start: 0.7554 (mp10) cc_final: 0.7151 (mp10) REVERT: J 32 TYR cc_start: 0.8751 (p90) cc_final: 0.8550 (p90) REVERT: K 4 MET cc_start: 0.9035 (mmm) cc_final: 0.8745 (mmm) REVERT: K 54 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7623 (tmm-80) REVERT: E 95 TYR cc_start: 0.7576 (m-80) cc_final: 0.7126 (m-80) REVERT: F 4 MET cc_start: 0.6071 (mtp) cc_final: 0.5632 (mtp) outliers start: 66 outliers final: 29 residues processed: 383 average time/residue: 0.4250 time to fit residues: 252.9922 Evaluate side-chains 317 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1000 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 801 GLN Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain F residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 347 optimal weight: 8.9990 chunk 286 optimal weight: 0.8980 chunk 319 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 258 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN H 59 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 89 GLN E 27 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29042 Z= 0.315 Angle : 0.588 9.554 39557 Z= 0.298 Chirality : 0.044 0.231 4629 Planarity : 0.004 0.051 5043 Dihedral : 6.010 56.621 4757 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 3.08 % Allowed : 9.85 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.20 (0.14), residues: 3531 helix: 2.07 (0.20), residues: 669 sheet: 0.13 (0.17), residues: 895 loop : -0.52 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 104 HIS 0.006 0.001 HIS A1061 PHE 0.022 0.002 PHE C 32 TYR 0.019 0.002 TYR B 348 ARG 0.009 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 308 time to evaluate : 3.322 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: A 104 TRP cc_start: 0.7923 (m-90) cc_final: 0.7413 (m-90) REVERT: A 224 GLU cc_start: 0.8783 (pm20) cc_final: 0.8536 (pm20) REVERT: A 272 PHE cc_start: 0.8501 (m-80) cc_final: 0.8286 (m-10) REVERT: A 335 PHE cc_start: 0.9101 (m-10) cc_final: 0.8774 (m-10) REVERT: A 448 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.5008 (t80) REVERT: A 449 LEU cc_start: 0.9746 (mt) cc_final: 0.9217 (tt) REVERT: A 494 PHE cc_start: 0.8054 (m-80) cc_final: 0.7549 (m-80) REVERT: A 579 LEU cc_start: 0.8681 (mt) cc_final: 0.8357 (pt) REVERT: A 581 ILE cc_start: 0.8464 (mm) cc_final: 0.7779 (tt) REVERT: A 866 MET cc_start: 0.8450 (mtt) cc_final: 0.8172 (mtt) REVERT: A 952 ASN cc_start: 0.7931 (t0) cc_final: 0.7515 (t0) REVERT: B 104 TRP cc_start: 0.6605 (m-90) cc_final: 0.6322 (m-90) REVERT: B 295 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: B 335 PHE cc_start: 0.8098 (m-80) cc_final: 0.7736 (m-80) REVERT: B 348 TYR cc_start: 0.9312 (p90) cc_final: 0.8951 (p90) REVERT: B 433 TRP cc_start: 0.7338 (p90) cc_final: 0.6912 (p90) REVERT: B 855 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 987 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: B 1026 MET cc_start: 0.8712 (tpp) cc_final: 0.7956 (ttm) REVERT: C 206 LYS cc_start: 0.8647 (tptt) cc_final: 0.8391 (tptt) REVERT: C 399 ILE cc_start: 0.7901 (pt) cc_final: 0.7548 (pt) REVERT: C 405 ARG cc_start: 0.8182 (ppt170) cc_final: 0.7730 (ppt170) REVERT: C 433 TRP cc_start: 0.8296 (p90) cc_final: 0.7701 (p90) REVERT: C 446 TYR cc_start: 0.8922 (m-80) cc_final: 0.8710 (m-10) REVERT: C 461 PHE cc_start: 0.8921 (m-80) cc_final: 0.8679 (m-80) REVERT: C 581 ILE cc_start: 0.8473 (mm) cc_final: 0.7897 (mm) REVERT: C 855 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8827 (mt) REVERT: C 987 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 1001 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9249 (tt) REVERT: C 1047 MET cc_start: 0.8399 (ptp) cc_final: 0.8187 (ptp) REVERT: H 18 LEU cc_start: 0.8837 (tp) cc_final: 0.8601 (tt) REVERT: H 48 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6157 (mpp) REVERT: H 80 TYR cc_start: 0.9286 (m-80) cc_final: 0.9065 (m-80) REVERT: L 49 TYR cc_start: 0.8169 (p90) cc_final: 0.7762 (p90) REVERT: L 89 GLN cc_start: 0.3537 (OUTLIER) cc_final: 0.2239 (tp40) REVERT: J 48 MET cc_start: 0.8366 (mpp) cc_final: 0.8047 (mpp) REVERT: J 80 TYR cc_start: 0.8885 (m-80) cc_final: 0.8621 (t80) REVERT: J 106 LEU cc_start: 0.8815 (mt) cc_final: 0.8454 (mt) REVERT: K 4 MET cc_start: 0.9131 (mmm) cc_final: 0.8897 (mmm) REVERT: K 54 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7800 (ttp-170) REVERT: E 48 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.3941 (ppp) REVERT: E 64 PHE cc_start: 0.8747 (m-80) cc_final: 0.8483 (t80) REVERT: E 95 TYR cc_start: 0.7643 (m-80) cc_final: 0.7142 (m-80) REVERT: F 4 MET cc_start: 0.6094 (mtp) cc_final: 0.5701 (mtp) outliers start: 94 outliers final: 59 residues processed: 372 average time/residue: 0.4323 time to fit residues: 257.6086 Evaluate side-chains 342 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 274 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 40.0000 chunk 242 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 153 optimal weight: 0.0970 chunk 216 optimal weight: 0.0010 chunk 323 optimal weight: 4.9990 chunk 342 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS A 904 ASN A 946 GLN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 29042 Z= 0.159 Angle : 0.528 10.804 39557 Z= 0.267 Chirality : 0.043 0.237 4629 Planarity : 0.004 0.049 5043 Dihedral : 5.224 54.524 4757 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 2.13 % Allowed : 11.72 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.46 (0.14), residues: 3531 helix: 2.52 (0.20), residues: 656 sheet: 0.24 (0.17), residues: 890 loop : -0.40 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 350 HIS 0.005 0.001 HIS B1080 PHE 0.032 0.001 PHE F 71 TYR 0.032 0.001 TYR C 492 ARG 0.012 0.000 ARG C 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 318 time to evaluate : 3.482 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: A 104 TRP cc_start: 0.7922 (m-90) cc_final: 0.7385 (m-90) REVERT: A 135 PHE cc_start: 0.6222 (p90) cc_final: 0.5742 (p90) REVERT: A 224 GLU cc_start: 0.8769 (pm20) cc_final: 0.8540 (pm20) REVERT: A 335 PHE cc_start: 0.9067 (m-10) cc_final: 0.8721 (m-80) REVERT: A 448 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.5246 (t80) REVERT: A 579 LEU cc_start: 0.8624 (mt) cc_final: 0.8327 (pt) REVERT: A 581 ILE cc_start: 0.8405 (mm) cc_final: 0.7776 (tt) REVERT: A 866 MET cc_start: 0.8399 (mtt) cc_final: 0.8097 (mtt) REVERT: A 952 ASN cc_start: 0.7941 (t0) cc_final: 0.7469 (t0) REVERT: B 295 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: B 335 PHE cc_start: 0.7952 (m-80) cc_final: 0.7654 (m-80) REVERT: B 348 TYR cc_start: 0.9316 (p90) cc_final: 0.8968 (p90) REVERT: B 433 TRP cc_start: 0.7258 (p90) cc_final: 0.6840 (p90) REVERT: B 855 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7668 (mp) REVERT: B 987 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: B 1026 MET cc_start: 0.8580 (tpp) cc_final: 0.8040 (ttm) REVERT: C 266 TYR cc_start: 0.7574 (m-80) cc_final: 0.7179 (m-80) REVERT: C 389 PHE cc_start: 0.8073 (m-80) cc_final: 0.7740 (m-80) REVERT: C 399 ILE cc_start: 0.7991 (pt) cc_final: 0.7664 (pt) REVERT: C 405 ARG cc_start: 0.8189 (ppt170) cc_final: 0.7619 (ppt170) REVERT: C 446 TYR cc_start: 0.8888 (m-80) cc_final: 0.8668 (m-10) REVERT: C 581 ILE cc_start: 0.8398 (mm) cc_final: 0.7813 (mm) REVERT: C 1001 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9250 (tt) REVERT: H 80 TYR cc_start: 0.9405 (m-80) cc_final: 0.8864 (m-80) REVERT: L 45 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8420 (mmm160) REVERT: L 49 TYR cc_start: 0.8154 (p90) cc_final: 0.7808 (p90) REVERT: L 89 GLN cc_start: 0.4537 (OUTLIER) cc_final: 0.3817 (tp40) REVERT: J 80 TYR cc_start: 0.8905 (m-80) cc_final: 0.8667 (t80) REVERT: K 4 MET cc_start: 0.9119 (mmm) cc_final: 0.8838 (mmm) REVERT: K 54 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7843 (ttp-110) REVERT: E 95 TYR cc_start: 0.7668 (m-80) cc_final: 0.7178 (m-80) REVERT: F 4 MET cc_start: 0.6160 (mtp) cc_final: 0.5529 (mtp) outliers start: 65 outliers final: 40 residues processed: 357 average time/residue: 0.4175 time to fit residues: 236.9954 Evaluate side-chains 327 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 281 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 291 optimal weight: 30.0000 chunk 236 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 307 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN A 904 ASN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 29042 Z= 0.455 Angle : 0.642 10.225 39557 Z= 0.326 Chirality : 0.045 0.238 4629 Planarity : 0.004 0.061 5043 Dihedral : 5.274 52.917 4755 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 3.76 % Allowed : 11.75 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.15 (0.14), residues: 3531 helix: 1.94 (0.20), residues: 664 sheet: 0.10 (0.17), residues: 892 loop : -0.52 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.012 0.002 HIS J 99 PHE 0.029 0.002 PHE F 71 TYR 0.021 0.002 TYR B1064 ARG 0.006 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 284 time to evaluate : 3.521 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: A 104 TRP cc_start: 0.8107 (m-90) cc_final: 0.7563 (m-90) REVERT: A 224 GLU cc_start: 0.8879 (pm20) cc_final: 0.8661 (pm20) REVERT: A 335 PHE cc_start: 0.9094 (m-10) cc_final: 0.8797 (m-10) REVERT: A 448 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.5632 (t80) REVERT: A 494 PHE cc_start: 0.8748 (m-80) cc_final: 0.8385 (m-80) REVERT: A 579 LEU cc_start: 0.8742 (mt) cc_final: 0.8386 (pt) REVERT: A 866 MET cc_start: 0.8447 (mtt) cc_final: 0.8196 (mtt) REVERT: A 952 ASN cc_start: 0.8196 (t0) cc_final: 0.7761 (t0) REVERT: B 104 TRP cc_start: 0.7031 (m-90) cc_final: 0.6442 (m-90) REVERT: B 295 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: B 314 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (m-40) REVERT: B 335 PHE cc_start: 0.8153 (m-80) cc_final: 0.7786 (m-80) REVERT: B 348 TYR cc_start: 0.9381 (p90) cc_final: 0.9015 (p90) REVERT: B 433 TRP cc_start: 0.7449 (p90) cc_final: 0.6945 (p90) REVERT: B 855 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 987 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: B 1026 MET cc_start: 0.8877 (tpp) cc_final: 0.8235 (ttm) REVERT: C 53 ASP cc_start: 0.7549 (m-30) cc_final: 0.7040 (m-30) REVERT: C 206 LYS cc_start: 0.8851 (tptt) cc_final: 0.8646 (tptt) REVERT: C 399 ILE cc_start: 0.8191 (pt) cc_final: 0.7911 (pt) REVERT: C 411 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8128 (tp-100) REVERT: C 433 TRP cc_start: 0.8374 (p90) cc_final: 0.7444 (p90) REVERT: C 446 TYR cc_start: 0.8900 (m-80) cc_final: 0.8682 (m-10) REVERT: C 461 PHE cc_start: 0.8935 (m-80) cc_final: 0.8695 (m-80) REVERT: C 492 TYR cc_start: 0.5772 (m-80) cc_final: 0.5267 (m-80) REVERT: C 581 ILE cc_start: 0.8469 (mm) cc_final: 0.7870 (mm) REVERT: C 705 SER cc_start: 0.8753 (p) cc_final: 0.8358 (m) REVERT: C 855 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8816 (mt) REVERT: C 987 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 1001 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9266 (tt) REVERT: C 1026 MET cc_start: 0.8928 (tpp) cc_final: 0.8321 (ttm) REVERT: H 38 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8496 (ttt-90) REVERT: H 46 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8194 (pp20) REVERT: H 64 PHE cc_start: 0.8446 (m-80) cc_final: 0.8046 (m-80) REVERT: H 80 TYR cc_start: 0.9386 (m-80) cc_final: 0.8804 (m-80) REVERT: L 45 ARG cc_start: 0.8785 (mmm160) cc_final: 0.8564 (mmm160) REVERT: L 49 TYR cc_start: 0.8195 (p90) cc_final: 0.7829 (p90) REVERT: L 58 ILE cc_start: 0.5317 (mm) cc_final: 0.4960 (mp) REVERT: J 4 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8951 (mp) REVERT: J 80 TYR cc_start: 0.8955 (m-80) cc_final: 0.8738 (t80) REVERT: K 4 MET cc_start: 0.9176 (mmm) cc_final: 0.7757 (mtp) REVERT: K 54 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7918 (ttp-110) REVERT: K 61 ARG cc_start: 0.4511 (mtp-110) cc_final: 0.3962 (ttp-110) REVERT: E 45 LEU cc_start: 0.8356 (mm) cc_final: 0.7923 (mm) REVERT: E 64 PHE cc_start: 0.8842 (m-80) cc_final: 0.8578 (t80) REVERT: E 95 TYR cc_start: 0.7676 (m-80) cc_final: 0.7134 (m-80) REVERT: F 4 MET cc_start: 0.6384 (mtp) cc_final: 0.5776 (mtp) outliers start: 115 outliers final: 78 residues processed: 370 average time/residue: 0.4182 time to fit residues: 251.5936 Evaluate side-chains 350 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 263 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1115 ASP Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 878 THR Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 2.9990 chunk 308 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 200 optimal weight: 30.0000 chunk 84 optimal weight: 0.5980 chunk 342 optimal weight: 8.9990 chunk 284 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 28 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29042 Z= 0.218 Angle : 0.551 12.825 39557 Z= 0.279 Chirality : 0.043 0.245 4629 Planarity : 0.004 0.050 5043 Dihedral : 4.941 49.444 4755 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 2.75 % Allowed : 13.19 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.31 (0.14), residues: 3531 helix: 2.32 (0.20), residues: 653 sheet: 0.15 (0.17), residues: 899 loop : -0.46 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 350 HIS 0.007 0.001 HIS H 67 PHE 0.023 0.001 PHE C 389 TYR 0.032 0.001 TYR H 60 ARG 0.006 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 298 time to evaluate : 3.030 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 104 TRP cc_start: 0.7979 (m-90) cc_final: 0.7495 (m-90) REVERT: A 135 PHE cc_start: 0.6332 (p90) cc_final: 0.5782 (p90) REVERT: A 224 GLU cc_start: 0.8866 (pm20) cc_final: 0.8567 (pm20) REVERT: A 323 ILE cc_start: 0.7079 (mt) cc_final: 0.6728 (tt) REVERT: A 335 PHE cc_start: 0.9051 (m-10) cc_final: 0.8749 (m-10) REVERT: A 393 TYR cc_start: 0.8870 (m-80) cc_final: 0.8586 (m-80) REVERT: A 448 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.5067 (t80) REVERT: A 449 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9275 (tt) REVERT: A 494 PHE cc_start: 0.8710 (m-80) cc_final: 0.8225 (m-80) REVERT: A 579 LEU cc_start: 0.8676 (mt) cc_final: 0.8393 (pt) REVERT: A 581 ILE cc_start: 0.8521 (mm) cc_final: 0.7848 (tt) REVERT: A 866 MET cc_start: 0.8411 (mtt) cc_final: 0.8142 (mtt) REVERT: A 952 ASN cc_start: 0.8164 (t0) cc_final: 0.7696 (t0) REVERT: B 295 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: B 314 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7914 (m-40) REVERT: B 335 PHE cc_start: 0.8024 (m-80) cc_final: 0.7690 (m-80) REVERT: B 348 TYR cc_start: 0.9379 (p90) cc_final: 0.8961 (p90) REVERT: B 433 TRP cc_start: 0.7404 (p90) cc_final: 0.6897 (p90) REVERT: B 777 GLU cc_start: 0.7754 (pt0) cc_final: 0.7445 (pt0) REVERT: B 855 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7703 (mp) REVERT: B 866 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7962 (ttm) REVERT: B 1026 MET cc_start: 0.8714 (tpp) cc_final: 0.7863 (ttm) REVERT: C 53 ASP cc_start: 0.7686 (m-30) cc_final: 0.7164 (m-30) REVERT: C 266 TYR cc_start: 0.7532 (m-80) cc_final: 0.6952 (m-80) REVERT: C 399 ILE cc_start: 0.8189 (pt) cc_final: 0.7788 (pt) REVERT: C 400 ARG cc_start: 0.8575 (mtp-110) cc_final: 0.8146 (mtp-110) REVERT: C 411 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8132 (tp-100) REVERT: C 433 TRP cc_start: 0.8278 (p90) cc_final: 0.7337 (p90) REVERT: C 446 TYR cc_start: 0.8882 (m-80) cc_final: 0.8649 (m-10) REVERT: C 492 TYR cc_start: 0.5579 (m-80) cc_final: 0.5019 (m-80) REVERT: C 581 ILE cc_start: 0.8407 (mm) cc_final: 0.7817 (mm) REVERT: C 855 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8730 (mt) REVERT: C 987 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7499 (tm-30) REVERT: C 1001 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9258 (tt) REVERT: C 1026 MET cc_start: 0.8883 (tpp) cc_final: 0.8231 (ttm) REVERT: H 64 PHE cc_start: 0.8344 (m-80) cc_final: 0.8043 (m-80) REVERT: H 80 TYR cc_start: 0.9334 (m-80) cc_final: 0.8970 (m-80) REVERT: L 58 ILE cc_start: 0.6268 (mm) cc_final: 0.6032 (mp) REVERT: L 89 GLN cc_start: 0.4388 (OUTLIER) cc_final: 0.2710 (tp40) REVERT: J 80 TYR cc_start: 0.8943 (m-80) cc_final: 0.8691 (t80) REVERT: J 106 LEU cc_start: 0.8990 (mt) cc_final: 0.8747 (mt) REVERT: K 4 MET cc_start: 0.9186 (mmm) cc_final: 0.7854 (mtp) REVERT: K 54 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7996 (ttp-110) REVERT: E 45 LEU cc_start: 0.8232 (mm) cc_final: 0.7776 (mm) REVERT: E 64 PHE cc_start: 0.8877 (m-80) cc_final: 0.8657 (t80) REVERT: E 95 TYR cc_start: 0.7751 (m-80) cc_final: 0.7169 (m-80) REVERT: F 4 MET cc_start: 0.6360 (mtp) cc_final: 0.5747 (mtp) outliers start: 84 outliers final: 51 residues processed: 358 average time/residue: 0.3963 time to fit residues: 228.3990 Evaluate side-chains 338 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 278 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 250 optimal weight: 0.3980 chunk 193 optimal weight: 0.0270 chunk 288 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN J 3 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29042 Z= 0.197 Angle : 0.546 13.451 39557 Z= 0.274 Chirality : 0.043 0.243 4629 Planarity : 0.004 0.052 5043 Dihedral : 4.719 49.319 4755 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.49 % Allowed : 13.88 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.42 (0.14), residues: 3531 helix: 2.56 (0.20), residues: 646 sheet: 0.20 (0.17), residues: 899 loop : -0.42 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 350 HIS 0.004 0.001 HIS H 67 PHE 0.028 0.001 PHE A 371 TYR 0.018 0.001 TYR C1135 ARG 0.005 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 289 time to evaluate : 3.119 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: A 104 TRP cc_start: 0.7951 (m-90) cc_final: 0.7535 (m-90) REVERT: A 224 GLU cc_start: 0.8866 (pm20) cc_final: 0.8580 (pm20) REVERT: A 323 ILE cc_start: 0.7156 (mt) cc_final: 0.6811 (tt) REVERT: A 335 PHE cc_start: 0.9032 (m-10) cc_final: 0.8714 (m-10) REVERT: A 393 TYR cc_start: 0.8886 (m-80) cc_final: 0.8605 (m-80) REVERT: A 448 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.5083 (t80) REVERT: A 449 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.9271 (tt) REVERT: A 494 PHE cc_start: 0.8672 (m-80) cc_final: 0.8193 (m-80) REVERT: A 579 LEU cc_start: 0.8688 (mt) cc_final: 0.8358 (pt) REVERT: A 581 ILE cc_start: 0.8528 (mm) cc_final: 0.7877 (tt) REVERT: A 866 MET cc_start: 0.8410 (mtt) cc_final: 0.8132 (mtt) REVERT: A 952 ASN cc_start: 0.8193 (t0) cc_final: 0.7741 (t0) REVERT: B 295 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: B 335 PHE cc_start: 0.7892 (m-80) cc_final: 0.7635 (m-80) REVERT: B 348 TYR cc_start: 0.9380 (p90) cc_final: 0.9024 (p90) REVERT: B 433 TRP cc_start: 0.7394 (p90) cc_final: 0.6881 (p90) REVERT: B 663 ILE cc_start: 0.8928 (mt) cc_final: 0.8703 (mt) REVERT: B 855 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7680 (mp) REVERT: B 866 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7957 (ttm) REVERT: B 1026 MET cc_start: 0.8700 (tpp) cc_final: 0.7979 (ttm) REVERT: C 53 ASP cc_start: 0.7742 (m-30) cc_final: 0.7035 (m-30) REVERT: C 54 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7975 (pp) REVERT: C 206 LYS cc_start: 0.8711 (tptt) cc_final: 0.8419 (tptp) REVERT: C 266 TYR cc_start: 0.7503 (m-80) cc_final: 0.7022 (m-80) REVERT: C 267 LEU cc_start: 0.8571 (pp) cc_final: 0.8275 (pp) REVERT: C 367 ASN cc_start: 0.8844 (m-40) cc_final: 0.8475 (p0) REVERT: C 399 ILE cc_start: 0.8112 (pt) cc_final: 0.7755 (pt) REVERT: C 400 ARG cc_start: 0.8581 (mtp-110) cc_final: 0.8173 (mtp-110) REVERT: C 405 ARG cc_start: 0.8239 (ppt170) cc_final: 0.7496 (ppt170) REVERT: C 433 TRP cc_start: 0.8264 (p90) cc_final: 0.7402 (p90) REVERT: C 446 TYR cc_start: 0.8905 (m-80) cc_final: 0.8654 (m-10) REVERT: C 492 TYR cc_start: 0.5547 (m-80) cc_final: 0.5025 (m-80) REVERT: C 581 ILE cc_start: 0.8407 (mm) cc_final: 0.7812 (mm) REVERT: C 855 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8719 (mt) REVERT: C 987 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7461 (tm-30) REVERT: C 1001 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9271 (tt) REVERT: C 1026 MET cc_start: 0.8875 (tpp) cc_final: 0.8281 (ttm) REVERT: H 80 TYR cc_start: 0.9317 (m-80) cc_final: 0.8935 (m-80) REVERT: L 45 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8282 (mmm160) REVERT: L 89 GLN cc_start: 0.4702 (OUTLIER) cc_final: 0.3359 (tp40) REVERT: J 80 TYR cc_start: 0.8964 (m-80) cc_final: 0.8739 (t80) REVERT: J 106 LEU cc_start: 0.8992 (mt) cc_final: 0.8739 (mt) REVERT: K 54 ARG cc_start: 0.8315 (mtt180) cc_final: 0.8090 (ttp-170) REVERT: E 45 LEU cc_start: 0.8136 (mm) cc_final: 0.7608 (mm) REVERT: E 64 PHE cc_start: 0.8896 (m-80) cc_final: 0.8677 (t80) REVERT: E 95 TYR cc_start: 0.7712 (m-80) cc_final: 0.7137 (m-80) REVERT: F 4 MET cc_start: 0.6335 (mtp) cc_final: 0.5731 (mtp) outliers start: 76 outliers final: 55 residues processed: 342 average time/residue: 0.4159 time to fit residues: 228.7555 Evaluate side-chains 342 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 278 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 909 THR Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 216 optimal weight: 0.5980 chunk 232 optimal weight: 20.0000 chunk 168 optimal weight: 0.6980 chunk 31 optimal weight: 30.0000 chunk 268 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29042 Z= 0.198 Angle : 0.546 12.832 39557 Z= 0.274 Chirality : 0.043 0.239 4629 Planarity : 0.004 0.054 5043 Dihedral : 4.513 49.029 4754 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 2.65 % Allowed : 14.04 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.50 (0.14), residues: 3531 helix: 2.62 (0.20), residues: 651 sheet: 0.27 (0.18), residues: 889 loop : -0.40 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 350 HIS 0.003 0.001 HIS E 27 PHE 0.021 0.001 PHE A 201 TYR 0.018 0.001 TYR A1064 ARG 0.010 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 284 time to evaluate : 3.264 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: A 104 TRP cc_start: 0.7960 (m-90) cc_final: 0.7594 (m-90) REVERT: A 224 GLU cc_start: 0.8867 (pm20) cc_final: 0.8600 (pm20) REVERT: A 323 ILE cc_start: 0.7255 (mt) cc_final: 0.6851 (tt) REVERT: A 335 PHE cc_start: 0.9030 (m-10) cc_final: 0.8712 (m-10) REVERT: A 393 TYR cc_start: 0.8898 (m-80) cc_final: 0.8623 (m-80) REVERT: A 448 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.4584 (t80) REVERT: A 449 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9275 (tt) REVERT: A 494 PHE cc_start: 0.8695 (m-80) cc_final: 0.7882 (m-80) REVERT: A 579 LEU cc_start: 0.8701 (mt) cc_final: 0.8365 (pt) REVERT: A 581 ILE cc_start: 0.8550 (mm) cc_final: 0.7912 (tt) REVERT: A 866 MET cc_start: 0.8411 (mtt) cc_final: 0.8136 (mtt) REVERT: A 952 ASN cc_start: 0.8216 (t0) cc_final: 0.7756 (t0) REVERT: B 295 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 335 PHE cc_start: 0.7890 (m-80) cc_final: 0.7622 (m-80) REVERT: B 348 TYR cc_start: 0.9368 (p90) cc_final: 0.8987 (p90) REVERT: B 433 TRP cc_start: 0.7413 (p90) cc_final: 0.6903 (p90) REVERT: B 855 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7735 (mp) REVERT: B 866 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7972 (ttm) REVERT: B 1026 MET cc_start: 0.8700 (tpp) cc_final: 0.7978 (ttm) REVERT: B 1038 ASP cc_start: 0.8185 (t0) cc_final: 0.7950 (t0) REVERT: C 53 ASP cc_start: 0.7881 (m-30) cc_final: 0.7135 (m-30) REVERT: C 54 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8006 (pp) REVERT: C 206 LYS cc_start: 0.8696 (tptt) cc_final: 0.8409 (tptp) REVERT: C 266 TYR cc_start: 0.7538 (m-80) cc_final: 0.7112 (m-80) REVERT: C 267 LEU cc_start: 0.8553 (pp) cc_final: 0.8296 (pp) REVERT: C 367 ASN cc_start: 0.8846 (m-40) cc_final: 0.8485 (p0) REVERT: C 399 ILE cc_start: 0.8102 (pt) cc_final: 0.7759 (pt) REVERT: C 405 ARG cc_start: 0.8270 (ppt170) cc_final: 0.7516 (ppt170) REVERT: C 433 TRP cc_start: 0.8242 (p90) cc_final: 0.7322 (p90) REVERT: C 446 TYR cc_start: 0.8918 (m-80) cc_final: 0.8661 (m-10) REVERT: C 449 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8207 (mp) REVERT: C 492 TYR cc_start: 0.5584 (m-80) cc_final: 0.5055 (m-80) REVERT: C 581 ILE cc_start: 0.8421 (mm) cc_final: 0.7830 (mm) REVERT: C 855 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8702 (mt) REVERT: C 1001 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9267 (tt) REVERT: C 1026 MET cc_start: 0.8868 (tpp) cc_final: 0.8287 (ttm) REVERT: H 80 TYR cc_start: 0.9279 (m-80) cc_final: 0.8896 (m-80) REVERT: L 45 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8457 (mmm160) REVERT: L 89 GLN cc_start: 0.4850 (OUTLIER) cc_final: 0.3837 (tp40) REVERT: J 80 TYR cc_start: 0.8946 (m-80) cc_final: 0.8713 (t80) REVERT: J 106 LEU cc_start: 0.8981 (mt) cc_final: 0.8592 (mt) REVERT: K 54 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7972 (tmm-80) REVERT: E 45 LEU cc_start: 0.8222 (mm) cc_final: 0.7720 (mm) REVERT: E 95 TYR cc_start: 0.7718 (m-80) cc_final: 0.7159 (m-80) REVERT: F 4 MET cc_start: 0.6287 (mtp) cc_final: 0.5674 (mtp) outliers start: 81 outliers final: 62 residues processed: 341 average time/residue: 0.3979 time to fit residues: 217.9214 Evaluate side-chains 344 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 272 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 695 SER Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 909 THR Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 30.0000 chunk 326 optimal weight: 50.0000 chunk 298 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 249 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 287 optimal weight: 2.9990 chunk 300 optimal weight: 40.0000 chunk 316 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 29042 Z= 0.431 Angle : 0.652 12.438 39557 Z= 0.328 Chirality : 0.045 0.242 4629 Planarity : 0.004 0.054 5043 Dihedral : 4.848 49.147 4754 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 2.78 % Allowed : 14.47 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.15 (0.14), residues: 3531 helix: 1.96 (0.20), residues: 659 sheet: 0.07 (0.18), residues: 880 loop : -0.49 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 350 HIS 0.008 0.001 HIS A1061 PHE 0.038 0.002 PHE B 559 TYR 0.023 0.002 TYR B1064 ARG 0.012 0.001 ARG C 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 271 time to evaluate : 3.259 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: A 104 TRP cc_start: 0.8055 (m-90) cc_final: 0.7697 (m-90) REVERT: A 224 GLU cc_start: 0.8966 (pm20) cc_final: 0.8687 (pm20) REVERT: A 335 PHE cc_start: 0.9074 (m-10) cc_final: 0.8701 (m-10) REVERT: A 393 TYR cc_start: 0.8900 (m-80) cc_final: 0.8560 (m-10) REVERT: A 448 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.4749 (t80) REVERT: A 449 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9287 (tt) REVERT: A 494 PHE cc_start: 0.8744 (m-80) cc_final: 0.7936 (m-80) REVERT: A 579 LEU cc_start: 0.8737 (mt) cc_final: 0.8435 (pt) REVERT: A 581 ILE cc_start: 0.8620 (mm) cc_final: 0.7919 (tt) REVERT: A 866 MET cc_start: 0.8432 (mtt) cc_final: 0.8181 (mtt) REVERT: B 295 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: B 335 PHE cc_start: 0.8092 (m-80) cc_final: 0.7843 (m-80) REVERT: B 348 TYR cc_start: 0.9415 (p90) cc_final: 0.8986 (p90) REVERT: B 354 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7240 (mtt180) REVERT: B 433 TRP cc_start: 0.7626 (p90) cc_final: 0.7038 (p90) REVERT: B 777 GLU cc_start: 0.7778 (pt0) cc_final: 0.7407 (pt0) REVERT: B 855 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 866 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8010 (ttm) REVERT: B 1026 MET cc_start: 0.8864 (tpp) cc_final: 0.8221 (ttm) REVERT: C 54 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8077 (pp) REVERT: C 206 LYS cc_start: 0.8799 (tptt) cc_final: 0.8516 (tptp) REVERT: C 266 TYR cc_start: 0.7584 (m-80) cc_final: 0.7207 (m-80) REVERT: C 267 LEU cc_start: 0.8602 (pp) cc_final: 0.8390 (pp) REVERT: C 324 VAL cc_start: 0.8176 (t) cc_final: 0.7663 (p) REVERT: C 399 ILE cc_start: 0.8190 (pt) cc_final: 0.7918 (pt) REVERT: C 411 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8184 (tp-100) REVERT: C 446 TYR cc_start: 0.8929 (m-80) cc_final: 0.8686 (m-10) REVERT: C 449 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 492 TYR cc_start: 0.5759 (m-80) cc_final: 0.5312 (m-80) REVERT: C 581 ILE cc_start: 0.8534 (mm) cc_final: 0.8019 (mm) REVERT: C 705 SER cc_start: 0.8740 (p) cc_final: 0.8393 (m) REVERT: C 855 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8812 (mt) REVERT: C 987 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 1001 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9267 (tt) REVERT: H 80 TYR cc_start: 0.9297 (m-80) cc_final: 0.9018 (m-80) REVERT: L 45 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8490 (mmm160) REVERT: J 106 LEU cc_start: 0.9035 (mt) cc_final: 0.8755 (mt) REVERT: K 54 ARG cc_start: 0.8337 (mtt180) cc_final: 0.8050 (ttp-110) REVERT: E 95 TYR cc_start: 0.7797 (m-80) cc_final: 0.7207 (m-80) REVERT: F 4 MET cc_start: 0.6448 (mtp) cc_final: 0.5762 (mtp) outliers start: 85 outliers final: 69 residues processed: 336 average time/residue: 0.3913 time to fit residues: 213.6946 Evaluate side-chains 336 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 258 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 909 THR Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 8.9990 chunk 336 optimal weight: 40.0000 chunk 205 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 324 optimal weight: 40.0000 chunk 280 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 29042 Z= 0.411 Angle : 0.779 59.199 39557 Z= 0.420 Chirality : 0.045 0.358 4629 Planarity : 0.005 0.068 5043 Dihedral : 4.832 49.115 4754 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 2.72 % Allowed : 14.80 % Favored : 82.49 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.69 % 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: 0.12 (0.14), residues: 3531 helix: 1.93 (0.20), residues: 659 sheet: 0.00 (0.18), residues: 890 loop : -0.49 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 350 HIS 0.006 0.001 HIS E 27 PHE 0.022 0.002 PHE B 540 TYR 0.068 0.002 TYR J 80 ARG 0.063 0.001 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7062 Ramachandran restraints generated. 3531 Oldfield, 0 Emsley, 3531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 258 time to evaluate : 4.313 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: A 104 TRP cc_start: 0.8048 (m-90) cc_final: 0.7685 (m-90) REVERT: A 224 GLU cc_start: 0.8962 (pm20) cc_final: 0.8684 (pm20) REVERT: A 335 PHE cc_start: 0.9069 (m-10) cc_final: 0.8700 (m-10) REVERT: A 393 TYR cc_start: 0.8903 (m-80) cc_final: 0.8558 (m-10) REVERT: A 448 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.4744 (t80) REVERT: A 449 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9287 (tt) REVERT: A 494 PHE cc_start: 0.8743 (m-80) cc_final: 0.7934 (m-80) REVERT: A 579 LEU cc_start: 0.8731 (mt) cc_final: 0.8433 (pt) REVERT: A 581 ILE cc_start: 0.8615 (mm) cc_final: 0.7917 (tt) REVERT: A 866 MET cc_start: 0.8425 (mtt) cc_final: 0.8173 (mtt) REVERT: B 295 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 335 PHE cc_start: 0.8173 (m-80) cc_final: 0.7866 (m-80) REVERT: B 348 TYR cc_start: 0.9414 (p90) cc_final: 0.8984 (p90) REVERT: B 354 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7230 (mtt180) REVERT: B 433 TRP cc_start: 0.7629 (p90) cc_final: 0.7035 (p90) REVERT: B 855 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7908 (mp) REVERT: B 866 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7996 (ttm) REVERT: B 1026 MET cc_start: 0.8852 (tpp) cc_final: 0.8211 (ttm) REVERT: C 54 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8068 (pp) REVERT: C 206 LYS cc_start: 0.8788 (tptt) cc_final: 0.8505 (tptp) REVERT: C 266 TYR cc_start: 0.7582 (m-80) cc_final: 0.7208 (m-80) REVERT: C 267 LEU cc_start: 0.8597 (pp) cc_final: 0.8372 (pp) REVERT: C 324 VAL cc_start: 0.8167 (t) cc_final: 0.7654 (p) REVERT: C 399 ILE cc_start: 0.8189 (pt) cc_final: 0.7917 (pt) REVERT: C 411 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8184 (tp-100) REVERT: C 446 TYR cc_start: 0.8927 (m-80) cc_final: 0.8687 (m-10) REVERT: C 449 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8332 (mp) REVERT: C 492 TYR cc_start: 0.5902 (m-80) cc_final: 0.5296 (m-80) REVERT: C 581 ILE cc_start: 0.8516 (mm) cc_final: 0.8001 (mm) REVERT: C 705 SER cc_start: 0.8736 (p) cc_final: 0.8376 (m) REVERT: C 855 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8796 (mt) REVERT: C 987 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 1001 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9266 (tt) REVERT: H 80 TYR cc_start: 0.9399 (m-80) cc_final: 0.9053 (m-80) REVERT: L 24 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8501 (mtm-85) REVERT: J 106 LEU cc_start: 0.9020 (mt) cc_final: 0.8746 (mt) REVERT: K 54 ARG cc_start: 0.8337 (mtt180) cc_final: 0.8043 (tmm-80) REVERT: E 95 TYR cc_start: 0.7794 (m-80) cc_final: 0.7206 (m-80) REVERT: F 4 MET cc_start: 0.6449 (mtp) cc_final: 0.5758 (mtp) outliers start: 83 outliers final: 71 residues processed: 321 average time/residue: 0.3880 time to fit residues: 202.4772 Evaluate side-chains 335 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 255 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 965 SER Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 540 PHE Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 ASP Chi-restraints excluded: chain B residue 985 GLU Chi-restraints excluded: chain B residue 1029 CYS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1124 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 544 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 728 MET Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 909 THR Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 965 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 93 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 258 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.149419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092592 restraints weight = 69972.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092831 restraints weight = 47335.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091585 restraints weight = 37033.778| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 29042 Z= 0.411 Angle : 0.779 59.199 39557 Z= 0.420 Chirality : 0.045 0.358 4629 Planarity : 0.005 0.068 5043 Dihedral : 4.832 49.115 4753 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 2.68 % Allowed : 14.89 % Favored : 82.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.69 % 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: 0.12 (0.14), residues: 3531 helix: 1.93 (0.20), residues: 659 sheet: 0.00 (0.18), residues: 890 loop : -0.49 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 350 HIS 0.006 0.001 HIS E 27 PHE 0.022 0.002 PHE B 540 TYR 0.068 0.002 TYR J 80 ARG 0.063 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5877.25 seconds wall clock time: 109 minutes 5.12 seconds (6545.12 seconds total)