Starting phenix.real_space_refine on Tue Mar 19 11:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/03_2024/7cn9_30419.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/03_2024/7cn9_30419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/03_2024/7cn9_30419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/03_2024/7cn9_30419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/03_2024/7cn9_30419.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cn9_30419/03_2024/7cn9_30419.pdb" } resolution = 4.7 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= 0.000 sd= 0.001 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 106 5.16 5 C 15304 2.51 5 N 3942 2.21 5 O 4700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 1111": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24052 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 7727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7727 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 48, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 7674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7674 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 48, 'TRANS': 961} Chain breaks: 10 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 164 Chain: "C" Number of atoms: 7889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 7889 Classifications: {'peptide': 1037} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 49, 'TRANS': 987} Chain breaks: 6 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 152 Chain: "E" 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: "X" 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: "k" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "p" 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: "W" 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: "Z" 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: "d" 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: "f" 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: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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 Chain: "H" 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: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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 Chain: "V" 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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 12.66, per 1000 atoms: 0.53 Number of scatterers: 24052 At special positions: 0 Unit cell: (152.52, 159.08, 167.28, 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 106 16.00 O 4700 8.00 N 3942 7.00 C 15304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.89 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.93 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.26 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 Atom "HETATM23770 O5 NAG A1203 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA h 3 " - " MAN h 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG N 1 " - " NAG N 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG k 1 " - " NAG k 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " BETA1-6 " NAG k 1 " - " FUC k 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1201 " - " ASN A 616 " " NAG A1202 " - " ASN A 657 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A1098 " " NAG A1205 " - " ASN A1134 " " NAG A1206 " - " ASN A 122 " " NAG A1207 " - " ASN A 282 " " NAG B1201 " - " ASN B 331 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 616 " " NAG B1204 " - " ASN B 657 " " NAG B1205 " - " ASN B 709 " " NAG B1206 " - " ASN B1098 " " NAG B1207 " - " ASN B 234 " " NAG B1208 " - " ASN B 165 " " NAG B1209 " - " ASN B 74 " " NAG C1201 " - " ASN C1134 " " NAG C1202 " - " ASN C 709 " " NAG C1203 " - " ASN C 657 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 61 " " NAG C1207 " - " ASN C 331 " " NAG E 1 " - " ASN C1074 " " NAG H 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 165 " " NAG Q 1 " - " ASN A 801 " " NAG V 1 " - " ASN A 331 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN C 717 " " NAG Z 1 " - " ASN B1134 " " NAG d 1 " - " ASN B1074 " " NAG f 1 " - " ASN B 801 " " NAG h 1 " - " ASN B 282 " " NAG k 1 " - " ASN C 165 " " NAG p 1 " - " ASN C 801 " Time building additional restraints: 9.64 Conformation dependent library (CDL) restraints added in 4.8 seconds 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5730 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 47 sheets defined 23.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.541A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.021A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.736A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.714A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.664A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 940 removed outlier: 6.068A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.512A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 4.586A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.785A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.456A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.195A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.081A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.485A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.540A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.767A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.290A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.866A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 940 removed outlier: 6.380A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 937 " --> pdb=" O LYS C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.883A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1034 removed outlier: 6.078A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.062A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.513A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 removed outlier: 3.901A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 205 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.012A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 572 through 573 removed outlier: 7.000A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.546A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AB4, first strand: chain 'A' and resid 724 through 728 removed outlier: 3.629A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A1049 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.604A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1086 through 1090 removed outlier: 5.419A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.745A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 192 through 194 removed outlier: 3.876A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.842A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.644A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 312 removed outlier: 3.879A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC7, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AC8, first strand: chain 'B' and resid 612 through 613 removed outlier: 3.703A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 659 through 660 removed outlier: 3.528A pdb=" N TYR B 660 " --> pdb=" O THR B 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.162A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1086 through 1088 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 4.236A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 4.299A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.710A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 326 through 328 removed outlier: 7.313A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.831A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 644 through 645 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.700A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 717 through 727 removed outlier: 3.712A pdb=" N VAL C1068 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 5.272A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1096 698 hydrogen bonds defined for protein. 1932 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: 8.66 Time building geometry restraints manager: 10.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7598 1.34 - 1.47: 6253 1.47 - 1.59: 10581 1.59 - 1.72: 3 1.72 - 1.85: 135 Bond restraints: 24570 Sorted by residual: bond pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 1.469 1.700 -0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 1.469 1.700 -0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 bond pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.09e+01 ... (remaining 24565 not shown) Histogram of bond angle deviations from ideal: 96.89 - 105.63: 528 105.63 - 114.37: 14807 114.37 - 123.11: 16370 123.11 - 131.85: 1751 131.85 - 140.60: 27 Bond angle restraints: 33483 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 119.84 140.60 -20.76 1.25e+00 6.40e-01 2.76e+02 angle pdb=" C PHE C 329 " pdb=" N PRO C 330 " pdb=" CA PRO C 330 " ideal model delta sigma weight residual 119.84 139.73 -19.89 1.25e+00 6.40e-01 2.53e+02 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 98.17 13.83 1.40e+00 5.10e-01 9.76e+01 angle pdb=" CA PRO C 330 " pdb=" N PRO C 330 " pdb=" CD PRO C 330 " ideal model delta sigma weight residual 112.00 99.76 12.24 1.40e+00 5.10e-01 7.64e+01 angle pdb=" C SER B 172 " pdb=" N GLN B 173 " pdb=" CA GLN B 173 " ideal model delta sigma weight residual 122.89 115.80 7.09 1.12e+00 7.97e-01 4.00e+01 ... (remaining 33478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.59: 14012 22.59 - 45.17: 1026 45.17 - 67.76: 176 67.76 - 90.34: 61 90.34 - 112.93: 16 Dihedral angle restraints: 15291 sinusoidal: 6407 harmonic: 8884 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.55 -80.45 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -6.43 -79.57 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 15288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4004 0.199 - 0.397: 26 0.397 - 0.596: 0 0.596 - 0.794: 3 0.794 - 0.993: 2 Chirality restraints: 4035 Sorted by residual: chirality pdb=" C1 BMA p 3 " pdb=" O4 NAG p 2 " pdb=" C2 BMA p 3 " pdb=" O5 BMA p 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.75e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.38e+01 ... (remaining 4032 not shown) Planarity restraints: 4286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 1 " -0.332 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG V 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG V 1 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG V 1 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG V 1 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " 0.275 2.00e-02 2.50e+03 2.30e-01 6.59e+02 pdb=" C7 NAG X 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " -0.386 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG p 1 " -0.257 2.00e-02 2.50e+03 2.15e-01 5.76e+02 pdb=" C7 NAG p 1 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG p 1 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG p 1 " 0.358 2.00e-02 2.50e+03 pdb=" O7 NAG p 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 4283 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 570 2.52 - 3.12: 22695 3.12 - 3.71: 37724 3.71 - 4.31: 50734 4.31 - 4.90: 76530 Nonbonded interactions: 188253 Sorted by model distance: nonbonded pdb=" O LEU C 455 " pdb=" CD1 PHE C 456 " model vdw 1.927 3.340 nonbonded pdb=" CZ PHE B 86 " pdb=" N GLY B 89 " model vdw 1.988 3.420 nonbonded pdb=" O SER C1003 " pdb=" OG1 THR C1006 " model vdw 2.004 2.440 nonbonded pdb=" O SER B1003 " pdb=" OG1 THR B1006 " model vdw 2.021 2.440 nonbonded pdb=" NE2 GLN B 613 " pdb=" OD1 ASP B 614 " model vdw 2.026 2.520 ... (remaining 188248 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 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 95 or (resid 96 throu \ gh 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (r \ esid 99 through 100 and (name N or name CA or name C or name O or name CB )) or \ resid 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 through 104 or (resid 105 and (name N or name CA or name C or name \ O or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 140 or (resid 141 and (nam \ e N or name CA or name C or name O or name CB )) or resid 142 through 155 or (re \ sid 156 and (name N or name CA or name C or name O or name CB )) or resid 157 th \ rough 159 or resid 165 through 175 or (resid 176 and (name N or name CA or name \ C or name O or name CB )) or (resid 187 and (name N or name CA or name C or name \ O or name CB )) or resid 188 through 194 or (resid 195 through 198 and (name N \ or name CA or name C or name O or name CB )) or resid 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 236 or (re \ sid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 or \ (resid 239 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 0 through 243 or resid 264 through 331 or (resid 332 through 333 and (name N or \ name CA or name C or name O or name CB )) or resid 334 or (resid 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 343 or resid \ 355 through 363 or (resid 364 and (name N or name CA or name C or name O or name \ CB )) or resid 365 through 368 or (resid 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 373 or (resid 374 and (name N or nam \ e CA or name C or name O or name CB )) or resid 375 through 407 or (resid 408 an \ d (name N or name CA or name C or name O or name CB )) or resid 409 through 442 \ or resid 455 or (resid 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 496 or (resid 497 through 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 through 500 or resid 503 through 50 \ 4 or (resid 505 and (name N or name CA or name C or name O or name CB )) or resi \ d 506 through 508 or (resid 509 and (name N or name CA or name C or name O or na \ me CB )) or resid 510 through 620 or resid 640 through 672 or resid 687 through \ 1140 or resid 1201 through 1207)) selection = (chain 'B' and (resid 27 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 159 or resid 165 t \ hrough 175 or (resid 176 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 189 or (resid 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 209 or (resid 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 or (resid 212 through 215 and (name N or n \ ame CA or name C or name O or name CB )) or resid 216 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 or (resid \ 239 and (name N or name CA or name C or name O or name CB )) or resid 240 throug \ h 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) or \ resid 291 through 363 or (resid 364 and (name N or name CA or name C or name O o \ r name CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or na \ me C or name O or name CB )) or resid 375 through 442 or resid 452 or resid 454 \ or resid 462 through 463 or resid 492 through 496 or (resid 497 through 498 and \ (name N or name CA or name C or name O or name CB )) or resid 499 through 508 or \ (resid 509 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 0 through 527 or (resid 528 through 529 and (name N or name CA or name C or name \ O or name CB )) or resid 530 through 543 or (resid 544 and (name N or name CA o \ r name C or name O or name CB )) or resid 545 through 620 or resid 640 through 8 \ 11 or resid 815 through 1140 or resid 1201 through 1207)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 81 or re \ sid 83 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA o \ r name C or name O or name CB )) or resid 101 through 104 or (resid 105 and (nam \ e N or name CA or name C or name O or name CB )) or resid 106 through 139 or (re \ sid 140 through 141 and (name N or name CA or name C or name O or name CB )) or \ resid 142 through 155 or (resid 156 and (name N or name CA or name C or name O o \ r name CB )) or resid 157 through 158 or (resid 159 and (name N or name CA or na \ me C or name O or name CB )) or resid 165 through 199 or (resid 200 and (name N \ or name CA or name C or name O or name CB )) or resid 201 through 243 or resid 2 \ 64 through 331 or (resid 332 through 333 and (name N or name CA or name C or nam \ e O or name CB )) or resid 334 or (resid 335 and (name N or name CA or name C or \ name O or name CB )) or resid 336 through 343 or resid 355 through 402 or (resi \ d 403 and (name N or name CA or name C or name O or name CB )) or resid 404 thro \ ugh 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) o \ r resid 442 or resid 455 or (resid 457 and (name N or name CA or name C or name \ O or name CB )) or resid 458 or resid 491 through 500 or resid 503 through 504 o \ r (resid 505 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 06 through 543 or (resid 544 and (name N or name CA or name C or name O or name \ CB )) or resid 545 through 620 or resid 640 through 672 or resid 687 through 811 \ or resid 815 through 1140 or resid 1201 through 1207)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'N' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'Q' selection = chain 'h' } ncs_group { reference = (chain 'V' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) } 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.890 Check model and map are aligned: 0.370 Set scattering table: 0.180 Process input model: 65.640 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.190 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.011 0.232 24570 Z= 0.699 Angle : 1.185 20.755 33483 Z= 0.677 Chirality : 0.067 0.993 4035 Planarity : 0.010 0.288 4250 Dihedral : 16.720 112.925 9456 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 47.47 Ramachandran Plot: Outliers : 1.13 % Allowed : 21.36 % Favored : 77.51 % Rotamer: Outliers : 2.39 % Allowed : 16.18 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.89 (0.11), residues: 3006 helix: -3.38 (0.14), residues: 625 sheet: -3.19 (0.22), residues: 384 loop : -4.58 (0.10), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 64 HIS 0.013 0.002 HIS C1058 PHE 0.041 0.003 PHE B 515 TYR 0.036 0.004 TYR B 313 ARG 0.009 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 612 time to evaluate : 2.632 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: A 48 LEU cc_start: 0.8693 (tp) cc_final: 0.8329 (tp) REVERT: A 145 TYR cc_start: 0.6939 (m-10) cc_final: 0.6723 (m-10) REVERT: A 153 MET cc_start: 0.4748 (OUTLIER) cc_final: 0.3999 (tmm) REVERT: A 369 TYR cc_start: 0.6319 (t80) cc_final: 0.5259 (m-80) REVERT: A 391 CYS cc_start: 0.1014 (OUTLIER) cc_final: 0.0701 (p) REVERT: A 595 VAL cc_start: 0.8962 (t) cc_final: 0.8708 (p) REVERT: A 726 ILE cc_start: 0.9132 (pt) cc_final: 0.8907 (pt) REVERT: A 733 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8694 (mppt) REVERT: A 779 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9040 (tm-30) REVERT: A 790 LYS cc_start: 0.7729 (pttm) cc_final: 0.6815 (mmtm) REVERT: A 868 GLU cc_start: 0.8303 (pm20) cc_final: 0.7339 (tm-30) REVERT: A 873 TYR cc_start: 0.9210 (m-80) cc_final: 0.8891 (m-80) REVERT: A 984 LEU cc_start: 0.8624 (mp) cc_final: 0.8389 (mp) REVERT: A 1010 GLN cc_start: 0.8889 (mp10) cc_final: 0.8557 (mp10) REVERT: A 1036 GLN cc_start: 0.8763 (tt0) cc_final: 0.7436 (pt0) REVERT: A 1047 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7245 (m-10) REVERT: A 1113 GLN cc_start: 0.8676 (mt0) cc_final: 0.8448 (mt0) REVERT: B 32 PHE cc_start: 0.3453 (OUTLIER) cc_final: 0.2496 (m-10) REVERT: B 69 HIS cc_start: 0.6645 (m90) cc_final: 0.6403 (m170) REVERT: B 131 CYS cc_start: 0.6847 (OUTLIER) cc_final: 0.4981 (t) REVERT: B 153 MET cc_start: 0.7729 (mtm) cc_final: 0.6767 (tpt) REVERT: B 280 ASN cc_start: 0.8350 (t0) cc_final: 0.7966 (p0) REVERT: B 318 PHE cc_start: 0.8205 (p90) cc_final: 0.7812 (p90) REVERT: B 378 LYS cc_start: 0.6113 (mmtt) cc_final: 0.5704 (mmmt) REVERT: B 395 VAL cc_start: 0.8856 (t) cc_final: 0.8532 (t) REVERT: B 731 MET cc_start: 0.8064 (ttt) cc_final: 0.7714 (ttt) REVERT: B 780 GLU cc_start: 0.8490 (pt0) cc_final: 0.8260 (pt0) REVERT: B 821 LEU cc_start: 0.9302 (tp) cc_final: 0.8419 (tp) REVERT: B 825 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8737 (mtpt) REVERT: B 864 LEU cc_start: 0.9393 (tp) cc_final: 0.9176 (tp) REVERT: B 869 MET cc_start: 0.9076 (tpt) cc_final: 0.8658 (tpp) REVERT: B 902 MET cc_start: 0.8798 (mmp) cc_final: 0.8214 (mmp) REVERT: B 977 LEU cc_start: 0.8881 (pt) cc_final: 0.8622 (pp) REVERT: B 1010 GLN cc_start: 0.9308 (mt0) cc_final: 0.9011 (mt0) REVERT: B 1038 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8522 (mmtp) REVERT: B 1039 ARG cc_start: 0.8511 (ptm160) cc_final: 0.8265 (ptm160) REVERT: B 1095 PHE cc_start: 0.8958 (m-10) cc_final: 0.8635 (m-10) REVERT: B 1125 ASN cc_start: 0.8339 (p0) cc_final: 0.7941 (p0) REVERT: C 157 PHE cc_start: 0.5821 (m-80) cc_final: 0.4821 (t80) REVERT: C 200 TYR cc_start: 0.8112 (m-10) cc_final: 0.7894 (m-80) REVERT: C 278 LYS cc_start: 0.7388 (tttt) cc_final: 0.7170 (ttpp) REVERT: C 298 GLU cc_start: 0.9006 (mp0) cc_final: 0.8704 (mp0) REVERT: C 314 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 324 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 741 TYR cc_start: 0.9024 (t80) cc_final: 0.8781 (t80) REVERT: C 751 ASN cc_start: 0.8555 (t0) cc_final: 0.8136 (t0) REVERT: C 755 GLN cc_start: 0.7646 (mt0) cc_final: 0.7362 (mt0) REVERT: C 762 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8836 (tp-100) REVERT: C 764 ASN cc_start: 0.8580 (m-40) cc_final: 0.8267 (m-40) REVERT: C 780 GLU cc_start: 0.9017 (pt0) cc_final: 0.8795 (pt0) REVERT: C 919 ASN cc_start: 0.9220 (t0) cc_final: 0.8932 (t0) REVERT: C 923 ILE cc_start: 0.9451 (mm) cc_final: 0.9177 (mt) REVERT: C 1028 LYS cc_start: 0.9318 (mttm) cc_final: 0.8516 (mttp) REVERT: C 1039 ARG cc_start: 0.9159 (mtp180) cc_final: 0.8584 (mtp85) REVERT: C 1111 GLU cc_start: 0.8546 (tp30) cc_final: 0.8309 (tp30) REVERT: C 1113 GLN cc_start: 0.8992 (mp10) cc_final: 0.8517 (mp10) outliers start: 60 outliers final: 32 residues processed: 656 average time/residue: 0.3463 time to fit residues: 352.3709 Evaluate side-chains 549 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 512 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 40.0000 chunk 177 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 125 ASN A 134 GLN A 148 ASN A 188 ASN A 207 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 655 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 953 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1058 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS A1108 ASN B 49 HIS B 121 ASN B 317 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 564 GLN B 607 GLN B 613 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS C 506 GLN C 644 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24570 Z= 0.309 Angle : 0.879 12.486 33483 Z= 0.439 Chirality : 0.054 0.484 4035 Planarity : 0.006 0.072 4250 Dihedral : 11.770 110.132 4401 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.17 % Favored : 85.66 % Rotamer: Outliers : 0.24 % Allowed : 7.99 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.77 (0.12), residues: 3006 helix: -1.90 (0.18), residues: 620 sheet: -2.85 (0.23), residues: 406 loop : -3.95 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 886 HIS 0.009 0.002 HIS B1048 PHE 0.046 0.002 PHE C 140 TYR 0.035 0.002 TYR B 269 ARG 0.009 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 652 time to evaluate : 2.723 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: A 34 ARG cc_start: 0.7555 (mmp80) cc_final: 0.7278 (mmp80) REVERT: A 48 LEU cc_start: 0.8320 (tp) cc_final: 0.7760 (tp) REVERT: A 49 HIS cc_start: 0.7541 (t70) cc_final: 0.6728 (t-90) REVERT: A 153 MET cc_start: 0.5820 (ptt) cc_final: 0.5280 (tmm) REVERT: A 170 TYR cc_start: 0.8133 (t80) cc_final: 0.7920 (t80) REVERT: A 195 LYS cc_start: 0.8499 (ptmt) cc_final: 0.8259 (ptmt) REVERT: A 297 SER cc_start: 0.9462 (m) cc_final: 0.8967 (p) REVERT: A 369 TYR cc_start: 0.6241 (t80) cc_final: 0.5218 (m-80) REVERT: A 391 CYS cc_start: 0.1394 (OUTLIER) cc_final: 0.1066 (p) REVERT: A 595 VAL cc_start: 0.8909 (t) cc_final: 0.8542 (p) REVERT: A 598 ILE cc_start: 0.8992 (mt) cc_final: 0.8661 (tt) REVERT: A 726 ILE cc_start: 0.9225 (pt) cc_final: 0.8734 (pt) REVERT: A 742 ILE cc_start: 0.9352 (tp) cc_final: 0.9118 (tp) REVERT: A 779 GLN cc_start: 0.9318 (tm-30) cc_final: 0.9003 (tm-30) REVERT: A 790 LYS cc_start: 0.7467 (pttm) cc_final: 0.6730 (mmtm) REVERT: A 868 GLU cc_start: 0.8149 (pm20) cc_final: 0.7192 (tm-30) REVERT: A 901 GLN cc_start: 0.8752 (tt0) cc_final: 0.8550 (tt0) REVERT: A 902 MET cc_start: 0.8734 (mmp) cc_final: 0.8399 (mmp) REVERT: A 920 GLN cc_start: 0.8752 (pt0) cc_final: 0.8293 (tp40) REVERT: A 948 LEU cc_start: 0.9310 (mt) cc_final: 0.9041 (mt) REVERT: A 983 ARG cc_start: 0.8518 (ptt90) cc_final: 0.7860 (ptt90) REVERT: A 984 LEU cc_start: 0.8087 (mp) cc_final: 0.7832 (mp) REVERT: A 1036 GLN cc_start: 0.8663 (tt0) cc_final: 0.8111 (tt0) REVERT: A 1090 PRO cc_start: 0.9173 (Cg_endo) cc_final: 0.8938 (Cg_exo) REVERT: A 1113 GLN cc_start: 0.8669 (mt0) cc_final: 0.8446 (mt0) REVERT: B 58 PHE cc_start: 0.7877 (m-10) cc_final: 0.7161 (m-10) REVERT: B 69 HIS cc_start: 0.6309 (m90) cc_final: 0.6069 (m170) REVERT: B 153 MET cc_start: 0.7582 (mtm) cc_final: 0.6781 (tpt) REVERT: B 280 ASN cc_start: 0.8304 (t0) cc_final: 0.7874 (t0) REVERT: B 378 LYS cc_start: 0.6230 (mmtt) cc_final: 0.5869 (mmmt) REVERT: B 510 VAL cc_start: 0.8538 (p) cc_final: 0.8141 (m) REVERT: B 773 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8358 (tp30) REVERT: B 776 LYS cc_start: 0.9296 (ttpp) cc_final: 0.8657 (tmmt) REVERT: B 780 GLU cc_start: 0.8595 (pt0) cc_final: 0.7859 (pt0) REVERT: B 802 PHE cc_start: 0.7996 (m-80) cc_final: 0.7289 (m-80) REVERT: B 805 ILE cc_start: 0.9578 (mp) cc_final: 0.9345 (mp) REVERT: B 864 LEU cc_start: 0.9266 (tp) cc_final: 0.9042 (tp) REVERT: B 902 MET cc_start: 0.7687 (mmp) cc_final: 0.7104 (mmp) REVERT: B 965 GLN cc_start: 0.9039 (mm110) cc_final: 0.8697 (mm110) REVERT: B 1010 GLN cc_start: 0.9233 (mt0) cc_final: 0.8729 (mt0) REVERT: B 1028 LYS cc_start: 0.9144 (mttm) cc_final: 0.8793 (mtmt) REVERT: B 1036 GLN cc_start: 0.7893 (tt0) cc_final: 0.7612 (tt0) REVERT: B 1038 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8373 (mmtp) REVERT: B 1039 ARG cc_start: 0.8438 (ptm160) cc_final: 0.7670 (ptm160) REVERT: B 1052 PHE cc_start: 0.8288 (m-10) cc_final: 0.7867 (m-10) REVERT: B 1095 PHE cc_start: 0.8783 (m-10) cc_final: 0.7795 (m-10) REVERT: B 1125 ASN cc_start: 0.8200 (p0) cc_final: 0.7771 (p0) REVERT: C 153 MET cc_start: 0.6562 (ttm) cc_final: 0.6350 (ttm) REVERT: C 200 TYR cc_start: 0.7921 (m-10) cc_final: 0.7612 (m-80) REVERT: C 314 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8923 (tm-30) REVERT: C 324 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8166 (tm-30) REVERT: C 577 ARG cc_start: 0.8136 (ptp-110) cc_final: 0.7574 (ptp-170) REVERT: C 646 ARG cc_start: 0.8131 (tpt170) cc_final: 0.7808 (tpt170) REVERT: C 755 GLN cc_start: 0.7456 (mt0) cc_final: 0.7102 (mt0) REVERT: C 762 GLN cc_start: 0.8903 (tp-100) cc_final: 0.8635 (tp-100) REVERT: C 764 ASN cc_start: 0.8318 (m-40) cc_final: 0.7897 (m-40) REVERT: C 913 GLN cc_start: 0.8352 (mt0) cc_final: 0.8010 (mt0) REVERT: C 919 ASN cc_start: 0.9392 (t0) cc_final: 0.8982 (t0) REVERT: C 923 ILE cc_start: 0.9343 (mm) cc_final: 0.8680 (mm) REVERT: C 925 ASN cc_start: 0.9489 (t0) cc_final: 0.9218 (t0) REVERT: C 1010 GLN cc_start: 0.9008 (pm20) cc_final: 0.8614 (pm20) REVERT: C 1095 PHE cc_start: 0.8810 (m-10) cc_final: 0.7486 (m-10) REVERT: C 1109 PHE cc_start: 0.8918 (t80) cc_final: 0.8648 (t80) REVERT: C 1111 GLU cc_start: 0.8460 (tp30) cc_final: 0.7842 (tp30) REVERT: C 1113 GLN cc_start: 0.9026 (mp10) cc_final: 0.7858 (mp10) outliers start: 6 outliers final: 0 residues processed: 657 average time/residue: 0.3511 time to fit residues: 365.2584 Evaluate side-chains 554 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 277 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 275 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24570 Z= 0.284 Angle : 0.818 11.592 33483 Z= 0.406 Chirality : 0.051 0.394 4035 Planarity : 0.005 0.071 4250 Dihedral : 10.782 104.021 4401 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.07 % Favored : 84.73 % Rotamer: Outliers : 0.28 % Allowed : 5.61 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.21 (0.13), residues: 3006 helix: -1.12 (0.19), residues: 625 sheet: -2.57 (0.23), residues: 419 loop : -3.68 (0.11), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 886 HIS 0.007 0.002 HIS B 146 PHE 0.028 0.002 PHE C 823 TYR 0.045 0.002 TYR B 313 ARG 0.009 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 642 time to evaluate : 2.600 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: A 34 ARG cc_start: 0.7656 (mmp80) cc_final: 0.7345 (mmp80) REVERT: A 48 LEU cc_start: 0.8347 (tp) cc_final: 0.7815 (tp) REVERT: A 49 HIS cc_start: 0.7476 (t70) cc_final: 0.6773 (t70) REVERT: A 117 LEU cc_start: 0.8989 (tp) cc_final: 0.8757 (tp) REVERT: A 145 TYR cc_start: 0.7075 (m-10) cc_final: 0.6689 (m-80) REVERT: A 153 MET cc_start: 0.5595 (ptt) cc_final: 0.5090 (tmm) REVERT: A 170 TYR cc_start: 0.8141 (t80) cc_final: 0.7934 (t80) REVERT: A 195 LYS cc_start: 0.8410 (ptmt) cc_final: 0.8160 (ptmt) REVERT: A 250 THR cc_start: 0.7865 (p) cc_final: 0.7556 (t) REVERT: A 297 SER cc_start: 0.9431 (m) cc_final: 0.8914 (p) REVERT: A 369 TYR cc_start: 0.6188 (t80) cc_final: 0.5244 (m-80) REVERT: A 391 CYS cc_start: 0.1850 (OUTLIER) cc_final: 0.1608 (p) REVERT: A 595 VAL cc_start: 0.8864 (t) cc_final: 0.8515 (p) REVERT: A 598 ILE cc_start: 0.8999 (mt) cc_final: 0.8707 (tt) REVERT: A 726 ILE cc_start: 0.9184 (pt) cc_final: 0.8661 (pt) REVERT: A 779 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8939 (tm-30) REVERT: A 782 PHE cc_start: 0.9080 (m-80) cc_final: 0.8860 (m-80) REVERT: A 790 LYS cc_start: 0.7494 (pttm) cc_final: 0.6789 (mmtm) REVERT: A 868 GLU cc_start: 0.8262 (pm20) cc_final: 0.7088 (tm-30) REVERT: A 948 LEU cc_start: 0.9306 (mt) cc_final: 0.8999 (mt) REVERT: A 983 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8074 (ptt90) REVERT: A 1039 ARG cc_start: 0.8270 (ptp-170) cc_final: 0.7847 (ptp-170) REVERT: A 1090 PRO cc_start: 0.9175 (Cg_endo) cc_final: 0.8880 (Cg_exo) REVERT: A 1113 GLN cc_start: 0.8691 (mt0) cc_final: 0.8464 (mt0) REVERT: A 1121 PHE cc_start: 0.5789 (p90) cc_final: 0.5490 (p90) REVERT: B 69 HIS cc_start: 0.6136 (m90) cc_final: 0.5901 (m170) REVERT: B 152 TRP cc_start: 0.7940 (t60) cc_final: 0.7533 (t60) REVERT: B 153 MET cc_start: 0.7780 (mtm) cc_final: 0.6888 (tpt) REVERT: B 378 LYS cc_start: 0.6246 (mmtt) cc_final: 0.5830 (mmmt) REVERT: B 508 TYR cc_start: 0.6262 (OUTLIER) cc_final: 0.5598 (m-10) REVERT: B 727 LEU cc_start: 0.8960 (mt) cc_final: 0.8415 (mt) REVERT: B 773 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8965 (tp30) REVERT: B 776 LYS cc_start: 0.9322 (ttpp) cc_final: 0.8929 (tmmt) REVERT: B 802 PHE cc_start: 0.8100 (m-80) cc_final: 0.7735 (m-80) REVERT: B 902 MET cc_start: 0.7719 (mmp) cc_final: 0.6995 (mmp) REVERT: B 1010 GLN cc_start: 0.9185 (mt0) cc_final: 0.8592 (mt0) REVERT: B 1036 GLN cc_start: 0.7897 (tt0) cc_final: 0.7231 (mt0) REVERT: B 1038 LYS cc_start: 0.8776 (mppt) cc_final: 0.8508 (mmtt) REVERT: B 1039 ARG cc_start: 0.8049 (ptm160) cc_final: 0.7684 (ptm160) REVERT: B 1052 PHE cc_start: 0.8278 (m-10) cc_final: 0.7816 (m-10) REVERT: B 1095 PHE cc_start: 0.8617 (m-10) cc_final: 0.7611 (m-10) REVERT: B 1105 THR cc_start: 0.8935 (m) cc_final: 0.8691 (m) REVERT: B 1109 PHE cc_start: 0.9347 (t80) cc_final: 0.8487 (t80) REVERT: B 1110 TYR cc_start: 0.8403 (t80) cc_final: 0.8109 (t80) REVERT: C 314 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8991 (tm-30) REVERT: C 324 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 567 ARG cc_start: 0.5883 (pmt-80) cc_final: 0.5638 (pmt-80) REVERT: C 577 ARG cc_start: 0.8020 (ptp-110) cc_final: 0.7560 (ptp-170) REVERT: C 646 ARG cc_start: 0.8164 (tpt170) cc_final: 0.7813 (tpt170) REVERT: C 755 GLN cc_start: 0.7594 (mt0) cc_final: 0.7230 (mt0) REVERT: C 762 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8637 (tp-100) REVERT: C 764 ASN cc_start: 0.8341 (m-40) cc_final: 0.7984 (m-40) REVERT: C 780 GLU cc_start: 0.9045 (pt0) cc_final: 0.8833 (pt0) REVERT: C 919 ASN cc_start: 0.9455 (t0) cc_final: 0.9134 (t0) REVERT: C 923 ILE cc_start: 0.9305 (mm) cc_final: 0.8993 (mt) REVERT: C 925 ASN cc_start: 0.9460 (t0) cc_final: 0.9148 (t0) REVERT: C 1000 ARG cc_start: 0.9051 (mtt180) cc_final: 0.8495 (mtp85) REVERT: C 1004 LEU cc_start: 0.9363 (tp) cc_final: 0.9136 (tp) REVERT: C 1050 MET cc_start: 0.8807 (ppp) cc_final: 0.8349 (ppp) REVERT: C 1081 ILE cc_start: 0.8654 (mm) cc_final: 0.8448 (mm) REVERT: C 1111 GLU cc_start: 0.8649 (tp30) cc_final: 0.8165 (tp30) REVERT: C 1113 GLN cc_start: 0.8984 (mp10) cc_final: 0.7906 (mp10) outliers start: 7 outliers final: 1 residues processed: 648 average time/residue: 0.3311 time to fit residues: 338.4268 Evaluate side-chains 541 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 538 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 144 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 186 optimal weight: 5.9990 chunk 278 optimal weight: 0.6980 chunk 294 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS A1088 HIS B 87 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24570 Z= 0.251 Angle : 0.780 10.780 33483 Z= 0.388 Chirality : 0.050 0.501 4035 Planarity : 0.005 0.070 4250 Dihedral : 10.172 105.263 4401 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.57 % Favored : 86.29 % Rotamer: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.13), residues: 3006 helix: -0.73 (0.20), residues: 619 sheet: -2.46 (0.24), residues: 420 loop : -3.50 (0.12), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 64 HIS 0.016 0.002 HIS C 66 PHE 0.033 0.002 PHE B 559 TYR 0.026 0.002 TYR B 313 ARG 0.006 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 628 time to evaluate : 2.562 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 34 ARG cc_start: 0.7731 (mmp80) cc_final: 0.7460 (mmp80) REVERT: A 48 LEU cc_start: 0.8388 (tp) cc_final: 0.7972 (tp) REVERT: A 49 HIS cc_start: 0.7411 (t70) cc_final: 0.6668 (t70) REVERT: A 153 MET cc_start: 0.5485 (ptt) cc_final: 0.4999 (tmm) REVERT: A 195 LYS cc_start: 0.8298 (ptmt) cc_final: 0.8073 (ptmt) REVERT: A 297 SER cc_start: 0.9413 (m) cc_final: 0.8866 (p) REVERT: A 369 TYR cc_start: 0.6257 (t80) cc_final: 0.5283 (m-80) REVERT: A 595 VAL cc_start: 0.8837 (t) cc_final: 0.8465 (p) REVERT: A 598 ILE cc_start: 0.8969 (mt) cc_final: 0.8731 (tt) REVERT: A 726 ILE cc_start: 0.9163 (pt) cc_final: 0.8661 (pt) REVERT: A 737 ASP cc_start: 0.8636 (p0) cc_final: 0.8336 (p0) REVERT: A 740 MET cc_start: 0.7913 (mtt) cc_final: 0.7594 (mtt) REVERT: A 742 ILE cc_start: 0.9391 (tp) cc_final: 0.9173 (tp) REVERT: A 752 LEU cc_start: 0.7901 (mm) cc_final: 0.7673 (mm) REVERT: A 765 ARG cc_start: 0.8947 (mtm180) cc_final: 0.8602 (mtm180) REVERT: A 779 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8872 (tm-30) REVERT: A 782 PHE cc_start: 0.9012 (m-80) cc_final: 0.8676 (m-80) REVERT: A 790 LYS cc_start: 0.7430 (pttm) cc_final: 0.6867 (mmtm) REVERT: A 821 LEU cc_start: 0.8821 (pp) cc_final: 0.8598 (pp) REVERT: A 867 ASP cc_start: 0.8992 (p0) cc_final: 0.8703 (p0) REVERT: A 868 GLU cc_start: 0.8095 (pm20) cc_final: 0.7065 (tm-30) REVERT: A 902 MET cc_start: 0.8584 (mmp) cc_final: 0.8020 (mmp) REVERT: A 948 LEU cc_start: 0.9289 (mt) cc_final: 0.8947 (mt) REVERT: A 983 ARG cc_start: 0.8564 (ptt90) cc_final: 0.7874 (ptt90) REVERT: A 1090 PRO cc_start: 0.9233 (Cg_endo) cc_final: 0.8943 (Cg_exo) REVERT: A 1113 GLN cc_start: 0.8719 (mt0) cc_final: 0.8456 (mt0) REVERT: A 1121 PHE cc_start: 0.5802 (p90) cc_final: 0.5569 (p90) REVERT: B 58 PHE cc_start: 0.7829 (m-10) cc_final: 0.7615 (m-10) REVERT: B 69 HIS cc_start: 0.6121 (m90) cc_final: 0.5850 (m170) REVERT: B 152 TRP cc_start: 0.8062 (t60) cc_final: 0.7742 (t60) REVERT: B 153 MET cc_start: 0.7764 (mtm) cc_final: 0.6902 (tpt) REVERT: B 378 LYS cc_start: 0.6273 (mmtt) cc_final: 0.5861 (mmmt) REVERT: B 737 ASP cc_start: 0.8523 (p0) cc_final: 0.8216 (p0) REVERT: B 773 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8739 (tp30) REVERT: B 776 LYS cc_start: 0.9202 (ttpp) cc_final: 0.8568 (tmmt) REVERT: B 780 GLU cc_start: 0.8466 (pt0) cc_final: 0.7809 (pt0) REVERT: B 802 PHE cc_start: 0.8096 (m-80) cc_final: 0.7730 (m-80) REVERT: B 861 LEU cc_start: 0.9619 (tt) cc_final: 0.9376 (tt) REVERT: B 902 MET cc_start: 0.7720 (mmp) cc_final: 0.7241 (mmp) REVERT: B 1007 TYR cc_start: 0.9074 (t80) cc_final: 0.8867 (t80) REVERT: B 1010 GLN cc_start: 0.9003 (mt0) cc_final: 0.8670 (mt0) REVERT: B 1038 LYS cc_start: 0.8840 (mppt) cc_final: 0.8618 (mmtt) REVERT: B 1039 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7736 (ptm160) REVERT: B 1052 PHE cc_start: 0.8329 (m-10) cc_final: 0.7878 (m-10) REVERT: B 1095 PHE cc_start: 0.8654 (m-10) cc_final: 0.7594 (m-10) REVERT: B 1110 TYR cc_start: 0.8272 (t80) cc_final: 0.8053 (t80) REVERT: C 200 TYR cc_start: 0.7762 (m-80) cc_final: 0.7288 (m-80) REVERT: C 314 GLN cc_start: 0.9258 (tm-30) cc_final: 0.9015 (tm-30) REVERT: C 577 ARG cc_start: 0.7963 (ptp-110) cc_final: 0.7486 (ptp-170) REVERT: C 671 CYS cc_start: 0.3161 (p) cc_final: 0.2382 (p) REVERT: C 731 MET cc_start: 0.8563 (ptm) cc_final: 0.7916 (tmm) REVERT: C 732 THR cc_start: 0.8827 (p) cc_final: 0.8549 (p) REVERT: C 741 TYR cc_start: 0.8778 (t80) cc_final: 0.8477 (t80) REVERT: C 755 GLN cc_start: 0.7559 (mt0) cc_final: 0.7229 (mt0) REVERT: C 764 ASN cc_start: 0.8328 (m-40) cc_final: 0.7986 (m-40) REVERT: C 780 GLU cc_start: 0.9043 (pt0) cc_final: 0.8771 (pt0) REVERT: C 919 ASN cc_start: 0.9491 (t0) cc_final: 0.9173 (t0) REVERT: C 923 ILE cc_start: 0.9318 (mm) cc_final: 0.8955 (mt) REVERT: C 925 ASN cc_start: 0.9451 (t0) cc_final: 0.9090 (t0) REVERT: C 1004 LEU cc_start: 0.9359 (tp) cc_final: 0.9109 (tp) REVERT: C 1010 GLN cc_start: 0.9033 (pm20) cc_final: 0.8669 (pm20) REVERT: C 1109 PHE cc_start: 0.8777 (t80) cc_final: 0.8574 (t80) REVERT: C 1111 GLU cc_start: 0.8693 (tp30) cc_final: 0.8171 (tp30) REVERT: C 1113 GLN cc_start: 0.8970 (mp10) cc_final: 0.7887 (mp10) REVERT: C 1135 ASN cc_start: 0.5565 (t0) cc_final: 0.5261 (t0) outliers start: 2 outliers final: 0 residues processed: 630 average time/residue: 0.3376 time to fit residues: 333.4392 Evaluate side-chains 538 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 4 optimal weight: 40.0000 chunk 219 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 203 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN B 955 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 658 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C 992 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24570 Z= 0.203 Angle : 0.743 10.027 33483 Z= 0.366 Chirality : 0.049 0.416 4035 Planarity : 0.005 0.074 4250 Dihedral : 9.483 104.780 4401 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.71 % Favored : 87.19 % Rotamer: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.14), residues: 3006 helix: -0.27 (0.20), residues: 614 sheet: -2.11 (0.25), residues: 402 loop : -3.33 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 PHE 0.026 0.002 PHE B 559 TYR 0.020 0.002 TYR B 313 ARG 0.010 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 638 time to evaluate : 2.772 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: A 48 LEU cc_start: 0.8281 (tp) cc_final: 0.7986 (tp) REVERT: A 49 HIS cc_start: 0.7106 (t70) cc_final: 0.6654 (t70) REVERT: A 117 LEU cc_start: 0.8858 (tp) cc_final: 0.8637 (tp) REVERT: A 145 TYR cc_start: 0.7156 (m-10) cc_final: 0.6724 (m-80) REVERT: A 153 MET cc_start: 0.5451 (ptt) cc_final: 0.4967 (tmm) REVERT: A 297 SER cc_start: 0.9381 (m) cc_final: 0.8953 (p) REVERT: A 302 THR cc_start: 0.8388 (t) cc_final: 0.8077 (t) REVERT: A 369 TYR cc_start: 0.6246 (t80) cc_final: 0.5277 (m-80) REVERT: A 598 ILE cc_start: 0.8943 (mt) cc_final: 0.8705 (tt) REVERT: A 696 THR cc_start: 0.8004 (m) cc_final: 0.7798 (m) REVERT: A 726 ILE cc_start: 0.9371 (pt) cc_final: 0.8860 (pt) REVERT: A 773 GLU cc_start: 0.8983 (pt0) cc_final: 0.8751 (pt0) REVERT: A 790 LYS cc_start: 0.7321 (pttm) cc_final: 0.6919 (mmtm) REVERT: A 867 ASP cc_start: 0.9001 (p0) cc_final: 0.8706 (p0) REVERT: A 868 GLU cc_start: 0.8101 (pm20) cc_final: 0.6951 (tm-30) REVERT: A 902 MET cc_start: 0.8515 (mmp) cc_final: 0.7907 (mmp) REVERT: A 920 GLN cc_start: 0.8684 (pt0) cc_final: 0.8219 (pm20) REVERT: A 948 LEU cc_start: 0.9265 (mt) cc_final: 0.8964 (mt) REVERT: A 969 ASN cc_start: 0.9192 (m-40) cc_final: 0.8791 (m-40) REVERT: A 983 ARG cc_start: 0.8645 (ptt90) cc_final: 0.8103 (ptt90) REVERT: A 1113 GLN cc_start: 0.8729 (mt0) cc_final: 0.8483 (mt0) REVERT: B 69 HIS cc_start: 0.6091 (m90) cc_final: 0.5864 (m170) REVERT: B 152 TRP cc_start: 0.7970 (t60) cc_final: 0.7734 (t60) REVERT: B 153 MET cc_start: 0.7784 (mtm) cc_final: 0.6980 (tpt) REVERT: B 210 ILE cc_start: 0.8731 (tp) cc_final: 0.8524 (tt) REVERT: B 378 LYS cc_start: 0.6326 (mmtt) cc_final: 0.5911 (mmmt) REVERT: B 737 ASP cc_start: 0.8383 (p0) cc_final: 0.8069 (p0) REVERT: B 773 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8729 (tp30) REVERT: B 776 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8676 (tmmt) REVERT: B 780 GLU cc_start: 0.8449 (pt0) cc_final: 0.7850 (pt0) REVERT: B 802 PHE cc_start: 0.7876 (m-80) cc_final: 0.7400 (m-80) REVERT: B 861 LEU cc_start: 0.9622 (tt) cc_final: 0.9402 (tt) REVERT: B 902 MET cc_start: 0.7617 (mmp) cc_final: 0.7131 (mmp) REVERT: B 949 GLN cc_start: 0.8656 (tp40) cc_final: 0.8180 (tp-100) REVERT: B 954 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8271 (mm-40) REVERT: B 1010 GLN cc_start: 0.8951 (mt0) cc_final: 0.8636 (mt0) REVERT: B 1038 LYS cc_start: 0.8837 (mppt) cc_final: 0.8632 (mmtt) REVERT: B 1039 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7720 (ptm160) REVERT: B 1052 PHE cc_start: 0.8312 (m-10) cc_final: 0.7934 (m-10) REVERT: B 1110 TYR cc_start: 0.8215 (t80) cc_final: 0.7934 (t80) REVERT: C 194 PHE cc_start: 0.7975 (m-80) cc_final: 0.7720 (m-10) REVERT: C 314 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8986 (tm-30) REVERT: C 646 ARG cc_start: 0.7970 (tpt170) cc_final: 0.7613 (tpt-90) REVERT: C 664 ILE cc_start: 0.8889 (mt) cc_final: 0.8099 (pt) REVERT: C 671 CYS cc_start: 0.3534 (p) cc_final: 0.1835 (p) REVERT: C 731 MET cc_start: 0.8447 (ptm) cc_final: 0.7807 (tmm) REVERT: C 732 THR cc_start: 0.8826 (p) cc_final: 0.8480 (p) REVERT: C 741 TYR cc_start: 0.8765 (t80) cc_final: 0.8339 (t80) REVERT: C 755 GLN cc_start: 0.7548 (mt0) cc_final: 0.7222 (mt0) REVERT: C 764 ASN cc_start: 0.8310 (m-40) cc_final: 0.7965 (m-40) REVERT: C 770 ILE cc_start: 0.8705 (pt) cc_final: 0.8495 (pt) REVERT: C 780 GLU cc_start: 0.9025 (pt0) cc_final: 0.8711 (pt0) REVERT: C 919 ASN cc_start: 0.9486 (t0) cc_final: 0.9147 (t0) REVERT: C 923 ILE cc_start: 0.9276 (mm) cc_final: 0.8904 (mt) REVERT: C 925 ASN cc_start: 0.9424 (t0) cc_final: 0.9054 (t0) REVERT: C 1010 GLN cc_start: 0.8863 (pm20) cc_final: 0.8525 (pm20) REVERT: C 1024 LEU cc_start: 0.8961 (tp) cc_final: 0.8338 (tp) REVERT: C 1028 LYS cc_start: 0.8921 (mttm) cc_final: 0.8474 (mttp) REVERT: C 1109 PHE cc_start: 0.8765 (t80) cc_final: 0.8512 (t80) REVERT: C 1111 GLU cc_start: 0.8614 (tp30) cc_final: 0.7961 (tp30) REVERT: C 1113 GLN cc_start: 0.8860 (mp10) cc_final: 0.7810 (mp10) outliers start: 1 outliers final: 0 residues processed: 639 average time/residue: 0.3412 time to fit residues: 345.4647 Evaluate side-chains 549 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS B 87 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 24570 Z= 0.389 Angle : 0.868 11.220 33483 Z= 0.436 Chirality : 0.053 0.487 4035 Planarity : 0.006 0.073 4250 Dihedral : 10.054 103.888 4401 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 26.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.83 % Favored : 84.10 % Rotamer: Outliers : 0.08 % Allowed : 3.78 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.14), residues: 3006 helix: -0.76 (0.19), residues: 626 sheet: -2.35 (0.24), residues: 412 loop : -3.38 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 64 HIS 0.010 0.002 HIS C1058 PHE 0.042 0.003 PHE B 559 TYR 0.025 0.003 TYR B 313 ARG 0.006 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 604 time to evaluate : 2.615 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: A 34 ARG cc_start: 0.7663 (mmp80) cc_final: 0.7380 (mmp80) REVERT: A 48 LEU cc_start: 0.8258 (tp) cc_final: 0.7922 (tp) REVERT: A 49 HIS cc_start: 0.7426 (t70) cc_final: 0.6856 (t70) REVERT: A 117 LEU cc_start: 0.8921 (tp) cc_final: 0.8713 (tp) REVERT: A 153 MET cc_start: 0.5473 (ptt) cc_final: 0.4999 (tmm) REVERT: A 195 LYS cc_start: 0.8278 (ptmt) cc_final: 0.8074 (ptmt) REVERT: A 297 SER cc_start: 0.9435 (m) cc_final: 0.8993 (p) REVERT: A 369 TYR cc_start: 0.6219 (t80) cc_final: 0.5243 (m-80) REVERT: A 598 ILE cc_start: 0.8881 (mt) cc_final: 0.8679 (tt) REVERT: A 726 ILE cc_start: 0.9273 (pt) cc_final: 0.8807 (pt) REVERT: A 742 ILE cc_start: 0.9471 (tp) cc_final: 0.9257 (tp) REVERT: A 777 ASN cc_start: 0.9340 (m110) cc_final: 0.9017 (m110) REVERT: A 779 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8918 (tm-30) REVERT: A 790 LYS cc_start: 0.7548 (pttm) cc_final: 0.6956 (mmtm) REVERT: A 867 ASP cc_start: 0.9174 (p0) cc_final: 0.8864 (p0) REVERT: A 868 GLU cc_start: 0.8205 (pm20) cc_final: 0.6851 (tm-30) REVERT: A 920 GLN cc_start: 0.8803 (pt0) cc_final: 0.8307 (pm20) REVERT: A 948 LEU cc_start: 0.9366 (mt) cc_final: 0.9005 (mt) REVERT: A 969 ASN cc_start: 0.9303 (m-40) cc_final: 0.8897 (m-40) REVERT: A 981 LEU cc_start: 0.9233 (tp) cc_final: 0.9008 (tt) REVERT: A 983 ARG cc_start: 0.8571 (ptt90) cc_final: 0.7823 (ptt90) REVERT: A 1113 GLN cc_start: 0.8711 (mt0) cc_final: 0.8454 (mt0) REVERT: B 152 TRP cc_start: 0.7999 (t60) cc_final: 0.7744 (t60) REVERT: B 153 MET cc_start: 0.7675 (mtm) cc_final: 0.6881 (tpt) REVERT: B 210 ILE cc_start: 0.8879 (tp) cc_final: 0.8323 (mp) REVERT: B 378 LYS cc_start: 0.6307 (mmtt) cc_final: 0.5871 (mmmt) REVERT: B 646 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7124 (tpp80) REVERT: B 727 LEU cc_start: 0.9060 (mt) cc_final: 0.8850 (mt) REVERT: B 737 ASP cc_start: 0.8636 (p0) cc_final: 0.8240 (p0) REVERT: B 773 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8647 (tp30) REVERT: B 776 LYS cc_start: 0.9164 (ttpp) cc_final: 0.8517 (tmmt) REVERT: B 780 GLU cc_start: 0.8582 (pt0) cc_final: 0.7979 (pt0) REVERT: B 861 LEU cc_start: 0.9629 (tt) cc_final: 0.9340 (tt) REVERT: B 902 MET cc_start: 0.7994 (mmp) cc_final: 0.7322 (mmp) REVERT: B 949 GLN cc_start: 0.8636 (tp40) cc_final: 0.8149 (tp-100) REVERT: B 1010 GLN cc_start: 0.9062 (mt0) cc_final: 0.8651 (mt0) REVERT: B 1038 LYS cc_start: 0.8834 (mppt) cc_final: 0.8630 (mmtt) REVERT: B 1039 ARG cc_start: 0.8174 (ptm160) cc_final: 0.7805 (ptm160) REVERT: B 1052 PHE cc_start: 0.8428 (m-10) cc_final: 0.7890 (m-10) REVERT: B 1064 HIS cc_start: 0.8424 (m-70) cc_final: 0.8172 (m-70) REVERT: B 1109 PHE cc_start: 0.9285 (t80) cc_final: 0.8209 (t80) REVERT: B 1110 TYR cc_start: 0.8312 (t80) cc_final: 0.7973 (t80) REVERT: C 152 TRP cc_start: 0.6763 (p-90) cc_final: 0.6089 (p-90) REVERT: C 194 PHE cc_start: 0.7844 (m-80) cc_final: 0.7623 (m-80) REVERT: C 314 GLN cc_start: 0.9325 (tm-30) cc_final: 0.9014 (tm-30) REVERT: C 429 PHE cc_start: 0.7472 (t80) cc_final: 0.7152 (p90) REVERT: C 664 ILE cc_start: 0.8828 (mt) cc_final: 0.8268 (pt) REVERT: C 731 MET cc_start: 0.8614 (ptm) cc_final: 0.8038 (tmm) REVERT: C 732 THR cc_start: 0.8795 (p) cc_final: 0.8503 (p) REVERT: C 741 TYR cc_start: 0.8811 (t80) cc_final: 0.8354 (t80) REVERT: C 755 GLN cc_start: 0.7724 (mt0) cc_final: 0.7454 (mt0) REVERT: C 762 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8756 (tp-100) REVERT: C 764 ASN cc_start: 0.8383 (m-40) cc_final: 0.7982 (m-40) REVERT: C 780 GLU cc_start: 0.9067 (pt0) cc_final: 0.8776 (pt0) REVERT: C 923 ILE cc_start: 0.9375 (mm) cc_final: 0.9128 (mm) REVERT: C 925 ASN cc_start: 0.9456 (t0) cc_final: 0.9136 (t0) REVERT: C 950 ASP cc_start: 0.8772 (m-30) cc_final: 0.8283 (m-30) REVERT: C 1004 LEU cc_start: 0.9434 (tp) cc_final: 0.9161 (tp) REVERT: C 1010 GLN cc_start: 0.9007 (pm20) cc_final: 0.8679 (pm20) REVERT: C 1109 PHE cc_start: 0.9002 (t80) cc_final: 0.8786 (t80) outliers start: 2 outliers final: 2 residues processed: 605 average time/residue: 0.3395 time to fit residues: 322.3575 Evaluate side-chains 519 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 517 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 6.9990 chunk 33 optimal weight: 0.0070 chunk 168 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 293 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 179 optimal weight: 0.3980 chunk 135 optimal weight: 8.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24570 Z= 0.194 Angle : 0.751 12.214 33483 Z= 0.369 Chirality : 0.050 0.469 4035 Planarity : 0.005 0.069 4250 Dihedral : 9.232 104.358 4401 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.38 % Favored : 88.52 % Rotamer: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.14), residues: 3006 helix: -0.24 (0.20), residues: 623 sheet: -1.92 (0.25), residues: 425 loop : -3.22 (0.12), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 886 HIS 0.007 0.001 HIS B1048 PHE 0.037 0.002 PHE B 823 TYR 0.019 0.002 TYR B1007 ARG 0.013 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 647 time to evaluate : 2.613 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: A 51 THR cc_start: 0.9278 (p) cc_final: 0.9065 (p) REVERT: A 117 LEU cc_start: 0.8854 (tp) cc_final: 0.8653 (tp) REVERT: A 145 TYR cc_start: 0.7046 (m-10) cc_final: 0.6814 (m-80) REVERT: A 153 MET cc_start: 0.5223 (ptt) cc_final: 0.4864 (tmm) REVERT: A 297 SER cc_start: 0.9428 (m) cc_final: 0.8978 (p) REVERT: A 369 TYR cc_start: 0.6168 (t80) cc_final: 0.5183 (m-80) REVERT: A 699 LEU cc_start: 0.9290 (mt) cc_final: 0.8851 (pt) REVERT: A 726 ILE cc_start: 0.9246 (pt) cc_final: 0.8737 (pt) REVERT: A 752 LEU cc_start: 0.8245 (mm) cc_final: 0.7651 (mm) REVERT: A 782 PHE cc_start: 0.8864 (m-80) cc_final: 0.8383 (m-80) REVERT: A 790 LYS cc_start: 0.7223 (pttm) cc_final: 0.6892 (mmtm) REVERT: A 867 ASP cc_start: 0.9141 (p0) cc_final: 0.8681 (p0) REVERT: A 868 GLU cc_start: 0.8079 (pm20) cc_final: 0.6657 (tm-30) REVERT: A 869 MET cc_start: 0.8797 (ptm) cc_final: 0.8303 (ppp) REVERT: A 902 MET cc_start: 0.8725 (mmp) cc_final: 0.8217 (mmp) REVERT: A 920 GLN cc_start: 0.8671 (pt0) cc_final: 0.8203 (pm20) REVERT: A 948 LEU cc_start: 0.9280 (mt) cc_final: 0.8959 (mt) REVERT: A 969 ASN cc_start: 0.9169 (m-40) cc_final: 0.8748 (m-40) REVERT: A 983 ARG cc_start: 0.8629 (ptt90) cc_final: 0.8121 (ptt90) REVERT: A 990 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 1067 TYR cc_start: 0.8041 (t80) cc_final: 0.7758 (t80) REVERT: A 1113 GLN cc_start: 0.8712 (mt0) cc_final: 0.8478 (mt0) REVERT: B 144 TYR cc_start: 0.5952 (m-10) cc_final: 0.5008 (p90) REVERT: B 152 TRP cc_start: 0.7957 (t60) cc_final: 0.7697 (t60) REVERT: B 153 MET cc_start: 0.7798 (mtm) cc_final: 0.6921 (tpt) REVERT: B 378 LYS cc_start: 0.6362 (mmtt) cc_final: 0.5937 (mmmt) REVERT: B 646 ARG cc_start: 0.7921 (ptm160) cc_final: 0.7190 (tpt170) REVERT: B 727 LEU cc_start: 0.8906 (mt) cc_final: 0.8598 (mt) REVERT: B 737 ASP cc_start: 0.8461 (p0) cc_final: 0.7997 (p0) REVERT: B 740 MET cc_start: 0.8487 (ttp) cc_final: 0.8213 (ttt) REVERT: B 762 GLN cc_start: 0.9062 (tm130) cc_final: 0.8787 (tm-30) REVERT: B 773 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8688 (tp30) REVERT: B 776 LYS cc_start: 0.9157 (ttpp) cc_final: 0.8676 (tmmt) REVERT: B 780 GLU cc_start: 0.8451 (pt0) cc_final: 0.7866 (pt0) REVERT: B 819 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 861 LEU cc_start: 0.9614 (tt) cc_final: 0.9381 (tt) REVERT: B 949 GLN cc_start: 0.8607 (tp40) cc_final: 0.8146 (tp-100) REVERT: B 957 GLN cc_start: 0.9037 (pp30) cc_final: 0.8775 (pp30) REVERT: B 1010 GLN cc_start: 0.8961 (mt0) cc_final: 0.8564 (mt0) REVERT: B 1052 PHE cc_start: 0.8416 (m-10) cc_final: 0.7930 (m-10) REVERT: B 1095 PHE cc_start: 0.8407 (m-10) cc_final: 0.7296 (m-10) REVERT: B 1110 TYR cc_start: 0.8113 (t80) cc_final: 0.7798 (t80) REVERT: C 152 TRP cc_start: 0.6859 (p-90) cc_final: 0.6198 (p-90) REVERT: C 314 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9085 (tm-30) REVERT: C 429 PHE cc_start: 0.7374 (t80) cc_final: 0.7154 (p90) REVERT: C 664 ILE cc_start: 0.8874 (mt) cc_final: 0.8128 (pt) REVERT: C 733 LYS cc_start: 0.9030 (pttm) cc_final: 0.8748 (pttm) REVERT: C 755 GLN cc_start: 0.7607 (mt0) cc_final: 0.7343 (mt0) REVERT: C 761 THR cc_start: 0.8505 (p) cc_final: 0.8284 (p) REVERT: C 764 ASN cc_start: 0.8259 (m-40) cc_final: 0.7996 (m-40) REVERT: C 774 GLN cc_start: 0.8211 (mt0) cc_final: 0.7746 (tt0) REVERT: C 780 GLU cc_start: 0.9039 (pt0) cc_final: 0.8729 (pt0) REVERT: C 909 ILE cc_start: 0.8509 (mm) cc_final: 0.8241 (mm) REVERT: C 917 TYR cc_start: 0.7356 (m-10) cc_final: 0.7083 (m-10) REVERT: C 925 ASN cc_start: 0.9369 (t0) cc_final: 0.8992 (t0) REVERT: C 1000 ARG cc_start: 0.9061 (mtt180) cc_final: 0.8627 (mtp85) REVERT: C 1004 LEU cc_start: 0.9280 (tp) cc_final: 0.9069 (tp) REVERT: C 1010 GLN cc_start: 0.8777 (pm20) cc_final: 0.8556 (pm20) REVERT: C 1065 VAL cc_start: 0.9076 (t) cc_final: 0.8810 (t) REVERT: C 1109 PHE cc_start: 0.8847 (t80) cc_final: 0.8544 (t80) REVERT: C 1111 GLU cc_start: 0.8449 (tp30) cc_final: 0.7827 (tp30) REVERT: C 1113 GLN cc_start: 0.8657 (mp10) cc_final: 0.7775 (mp10) outliers start: 1 outliers final: 1 residues processed: 648 average time/residue: 0.3435 time to fit residues: 350.1219 Evaluate side-chains 544 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 543 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 955 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24570 Z= 0.351 Angle : 0.825 11.473 33483 Z= 0.414 Chirality : 0.052 0.451 4035 Planarity : 0.006 0.077 4250 Dihedral : 9.617 104.198 4401 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.07 % Favored : 84.83 % Rotamer: Outliers : 0.04 % Allowed : 1.99 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.14), residues: 3006 helix: -0.42 (0.20), residues: 619 sheet: -2.02 (0.25), residues: 415 loop : -3.25 (0.12), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 886 HIS 0.009 0.002 HIS C1058 PHE 0.036 0.002 PHE B 823 TYR 0.026 0.002 TYR A1007 ARG 0.009 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 615 time to evaluate : 2.448 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: A 117 LEU cc_start: 0.8902 (tp) cc_final: 0.8673 (tp) REVERT: A 145 TYR cc_start: 0.7152 (m-10) cc_final: 0.6822 (m-80) REVERT: A 153 MET cc_start: 0.5336 (ptt) cc_final: 0.4992 (tmm) REVERT: A 297 SER cc_start: 0.9473 (m) cc_final: 0.9080 (p) REVERT: A 369 TYR cc_start: 0.6221 (t80) cc_final: 0.5214 (m-80) REVERT: A 737 ASP cc_start: 0.8549 (p0) cc_final: 0.8171 (p0) REVERT: A 752 LEU cc_start: 0.8266 (mm) cc_final: 0.7724 (mm) REVERT: A 790 LYS cc_start: 0.6921 (pttm) cc_final: 0.6617 (mmmm) REVERT: A 867 ASP cc_start: 0.9241 (p0) cc_final: 0.8819 (p0) REVERT: A 868 GLU cc_start: 0.8225 (pm20) cc_final: 0.6736 (tm-30) REVERT: A 869 MET cc_start: 0.8928 (ptm) cc_final: 0.8347 (ppp) REVERT: A 902 MET cc_start: 0.8829 (mmp) cc_final: 0.8465 (mmp) REVERT: A 969 ASN cc_start: 0.9283 (m-40) cc_final: 0.8827 (m-40) REVERT: A 981 LEU cc_start: 0.9268 (tp) cc_final: 0.9003 (tt) REVERT: A 983 ARG cc_start: 0.8588 (ptt90) cc_final: 0.7924 (ptt90) REVERT: A 990 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 1113 GLN cc_start: 0.8687 (mt0) cc_final: 0.8429 (mt0) REVERT: B 153 MET cc_start: 0.7658 (mtm) cc_final: 0.6871 (tpt) REVERT: B 378 LYS cc_start: 0.6317 (mmtt) cc_final: 0.5885 (mmmt) REVERT: B 646 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7319 (tpt170) REVERT: B 737 ASP cc_start: 0.8500 (p0) cc_final: 0.8050 (p0) REVERT: B 740 MET cc_start: 0.8489 (ttp) cc_final: 0.8172 (ttt) REVERT: B 773 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8664 (tp30) REVERT: B 776 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8557 (tmmt) REVERT: B 780 GLU cc_start: 0.8586 (pt0) cc_final: 0.7878 (pt0) REVERT: B 819 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8295 (pp20) REVERT: B 861 LEU cc_start: 0.9617 (tt) cc_final: 0.9310 (tt) REVERT: B 869 MET cc_start: 0.9367 (tpp) cc_final: 0.9086 (tpp) REVERT: B 949 GLN cc_start: 0.8528 (tp40) cc_final: 0.8158 (tp-100) REVERT: B 957 GLN cc_start: 0.9109 (pp30) cc_final: 0.8837 (pp30) REVERT: B 1010 GLN cc_start: 0.9008 (mt0) cc_final: 0.8773 (mt0) REVERT: B 1038 LYS cc_start: 0.8772 (mptt) cc_final: 0.8521 (mmtt) REVERT: B 1052 PHE cc_start: 0.8506 (m-10) cc_final: 0.8006 (m-10) REVERT: B 1105 THR cc_start: 0.8764 (m) cc_final: 0.8501 (m) REVERT: B 1109 PHE cc_start: 0.9230 (t80) cc_final: 0.8157 (t80) REVERT: B 1110 TYR cc_start: 0.8234 (t80) cc_final: 0.7849 (t80) REVERT: C 152 TRP cc_start: 0.6855 (p-90) cc_final: 0.6180 (p-90) REVERT: C 314 GLN cc_start: 0.9392 (tm-30) cc_final: 0.9052 (tm-30) REVERT: C 664 ILE cc_start: 0.8738 (mt) cc_final: 0.8124 (pt) REVERT: C 755 GLN cc_start: 0.7689 (mt0) cc_final: 0.7409 (mt0) REVERT: C 764 ASN cc_start: 0.8384 (m-40) cc_final: 0.8068 (m-40) REVERT: C 780 GLU cc_start: 0.9049 (pt0) cc_final: 0.8796 (pt0) REVERT: C 917 TYR cc_start: 0.7598 (m-10) cc_final: 0.6940 (m-10) REVERT: C 919 ASN cc_start: 0.9553 (t0) cc_final: 0.9278 (t0) REVERT: C 923 ILE cc_start: 0.9463 (mt) cc_final: 0.8911 (mt) REVERT: C 925 ASN cc_start: 0.9434 (t0) cc_final: 0.9115 (t0) REVERT: C 953 ASN cc_start: 0.8719 (m110) cc_final: 0.8516 (m-40) REVERT: C 1109 PHE cc_start: 0.9043 (t80) cc_final: 0.8746 (t80) outliers start: 1 outliers final: 1 residues processed: 616 average time/residue: 0.3405 time to fit residues: 330.5747 Evaluate side-chains 531 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 530 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 0.0570 chunk 281 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 259 optimal weight: 0.0270 chunk 272 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 774 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 954 GLN B 87 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 777 ASN B 784 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1054 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24570 Z= 0.190 Angle : 0.751 10.624 33483 Z= 0.369 Chirality : 0.050 0.432 4035 Planarity : 0.005 0.079 4250 Dihedral : 8.926 104.724 4401 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.81 % Favored : 89.09 % Rotamer: Outliers : 0.08 % Allowed : 0.80 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.14), residues: 3006 helix: -0.15 (0.20), residues: 623 sheet: -1.79 (0.25), residues: 422 loop : -3.11 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 886 HIS 0.007 0.001 HIS B1048 PHE 0.038 0.002 PHE C 823 TYR 0.022 0.001 TYR B1007 ARG 0.008 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 634 time to evaluate : 2.358 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 145 TYR cc_start: 0.7045 (m-10) cc_final: 0.6771 (m-80) REVERT: A 153 MET cc_start: 0.5323 (ptt) cc_final: 0.5067 (tmm) REVERT: A 297 SER cc_start: 0.9478 (m) cc_final: 0.9052 (p) REVERT: A 661 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8309 (mt-10) REVERT: A 737 ASP cc_start: 0.8363 (p0) cc_final: 0.7876 (p0) REVERT: A 742 ILE cc_start: 0.9426 (tp) cc_final: 0.9142 (tp) REVERT: A 782 PHE cc_start: 0.8924 (m-80) cc_final: 0.8594 (m-80) REVERT: A 790 LYS cc_start: 0.6949 (pttm) cc_final: 0.6590 (mmmm) REVERT: A 867 ASP cc_start: 0.9141 (p0) cc_final: 0.8685 (p0) REVERT: A 868 GLU cc_start: 0.8046 (pm20) cc_final: 0.6603 (tm-30) REVERT: A 869 MET cc_start: 0.8731 (ptm) cc_final: 0.8345 (ppp) REVERT: A 902 MET cc_start: 0.8710 (mmp) cc_final: 0.8311 (mmp) REVERT: A 920 GLN cc_start: 0.8720 (pt0) cc_final: 0.8071 (pm20) REVERT: A 923 ILE cc_start: 0.9269 (mt) cc_final: 0.8865 (mt) REVERT: A 926 GLN cc_start: 0.9115 (mt0) cc_final: 0.8569 (mp10) REVERT: A 969 ASN cc_start: 0.9131 (m-40) cc_final: 0.8701 (m-40) REVERT: A 983 ARG cc_start: 0.8587 (ptt90) cc_final: 0.8134 (ptt90) REVERT: A 990 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 1113 GLN cc_start: 0.8687 (mt0) cc_final: 0.8461 (mt0) REVERT: B 153 MET cc_start: 0.7718 (mtm) cc_final: 0.6906 (tpt) REVERT: B 378 LYS cc_start: 0.6474 (mmtt) cc_final: 0.6058 (mmmt) REVERT: B 727 LEU cc_start: 0.8855 (mt) cc_final: 0.8551 (mt) REVERT: B 737 ASP cc_start: 0.8275 (p0) cc_final: 0.7880 (p0) REVERT: B 740 MET cc_start: 0.8401 (ttp) cc_final: 0.8122 (ttt) REVERT: B 762 GLN cc_start: 0.9156 (tm130) cc_final: 0.8818 (tm-30) REVERT: B 773 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8714 (tp30) REVERT: B 776 LYS cc_start: 0.9194 (ttpp) cc_final: 0.8597 (tmmt) REVERT: B 780 GLU cc_start: 0.8469 (pt0) cc_final: 0.7850 (pt0) REVERT: B 861 LEU cc_start: 0.9609 (tt) cc_final: 0.9377 (tt) REVERT: B 949 GLN cc_start: 0.8452 (tp40) cc_final: 0.7789 (tp40) REVERT: B 954 GLN cc_start: 0.8500 (tp-100) cc_final: 0.7950 (tp-100) REVERT: B 1038 LYS cc_start: 0.8768 (mptt) cc_final: 0.8542 (mmtt) REVERT: B 1052 PHE cc_start: 0.8449 (m-10) cc_final: 0.8140 (m-10) REVERT: B 1095 PHE cc_start: 0.8296 (m-10) cc_final: 0.7063 (m-10) REVERT: B 1109 PHE cc_start: 0.9122 (t80) cc_final: 0.8081 (t80) REVERT: B 1110 TYR cc_start: 0.8105 (t80) cc_final: 0.7875 (t80) REVERT: C 58 PHE cc_start: 0.7197 (m-80) cc_final: 0.6397 (m-80) REVERT: C 152 TRP cc_start: 0.6858 (p-90) cc_final: 0.6223 (p-90) REVERT: C 314 GLN cc_start: 0.9393 (tm-30) cc_final: 0.9081 (tm-30) REVERT: C 776 LYS cc_start: 0.9163 (tmmt) cc_final: 0.8729 (tmmt) REVERT: C 780 GLU cc_start: 0.9056 (pt0) cc_final: 0.8563 (pt0) REVERT: C 781 VAL cc_start: 0.9780 (t) cc_final: 0.9575 (t) REVERT: C 919 ASN cc_start: 0.9530 (t0) cc_final: 0.9183 (t0) REVERT: C 923 ILE cc_start: 0.9472 (mt) cc_final: 0.8587 (mt) REVERT: C 925 ASN cc_start: 0.9343 (t0) cc_final: 0.8965 (t0) REVERT: C 1000 ARG cc_start: 0.9002 (mtt180) cc_final: 0.8493 (mtp85) REVERT: C 1010 GLN cc_start: 0.8841 (pm20) cc_final: 0.8567 (pm20) REVERT: C 1019 ARG cc_start: 0.9056 (mtp-110) cc_final: 0.8772 (ptm160) REVERT: C 1065 VAL cc_start: 0.9160 (t) cc_final: 0.8896 (t) REVERT: C 1109 PHE cc_start: 0.8897 (t80) cc_final: 0.8602 (t80) REVERT: C 1111 GLU cc_start: 0.8254 (tp30) cc_final: 0.7848 (tp30) REVERT: C 1113 GLN cc_start: 0.8225 (mp10) cc_final: 0.7516 (mp10) outliers start: 2 outliers final: 1 residues processed: 636 average time/residue: 0.3534 time to fit residues: 354.1315 Evaluate side-chains 541 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 540 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 303 optimal weight: 0.0980 chunk 279 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN A1083 HIS B 87 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24570 Z= 0.187 Angle : 0.725 12.411 33483 Z= 0.356 Chirality : 0.049 0.406 4035 Planarity : 0.005 0.081 4250 Dihedral : 8.542 102.418 4401 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.18 % Favored : 88.76 % Rotamer: Outliers : 0.04 % Allowed : 0.32 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.14), residues: 3006 helix: -0.11 (0.20), residues: 624 sheet: -1.71 (0.25), residues: 425 loop : -2.99 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 886 HIS 0.007 0.001 HIS C 66 PHE 0.050 0.002 PHE B 823 TYR 0.032 0.001 TYR B1007 ARG 0.013 0.001 ARG C 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6012 Ramachandran restraints generated. 3006 Oldfield, 0 Emsley, 3006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 648 time to evaluate : 2.356 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: A 34 ARG cc_start: 0.7779 (mmp80) cc_final: 0.7368 (mmp80) REVERT: A 117 LEU cc_start: 0.8920 (tp) cc_final: 0.8630 (tp) REVERT: A 145 TYR cc_start: 0.7128 (m-10) cc_final: 0.6759 (m-80) REVERT: A 170 TYR cc_start: 0.8048 (t80) cc_final: 0.7831 (t80) REVERT: A 297 SER cc_start: 0.9478 (m) cc_final: 0.9086 (p) REVERT: A 661 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8239 (mt-10) REVERT: A 737 ASP cc_start: 0.8242 (p0) cc_final: 0.7746 (p0) REVERT: A 742 ILE cc_start: 0.9439 (tp) cc_final: 0.9121 (tp) REVERT: A 790 LYS cc_start: 0.6992 (pttm) cc_final: 0.6646 (mmmm) REVERT: A 867 ASP cc_start: 0.9117 (p0) cc_final: 0.8645 (p0) REVERT: A 868 GLU cc_start: 0.8108 (pm20) cc_final: 0.6635 (tm-30) REVERT: A 869 MET cc_start: 0.8683 (ptm) cc_final: 0.8311 (ppp) REVERT: A 902 MET cc_start: 0.8744 (mmp) cc_final: 0.8310 (mmp) REVERT: A 920 GLN cc_start: 0.8716 (pt0) cc_final: 0.8184 (pm20) REVERT: A 923 ILE cc_start: 0.9268 (mt) cc_final: 0.8873 (mt) REVERT: A 926 GLN cc_start: 0.9135 (mt0) cc_final: 0.8598 (mp10) REVERT: A 969 ASN cc_start: 0.9084 (m-40) cc_final: 0.8602 (m-40) REVERT: A 983 ARG cc_start: 0.8604 (ptt90) cc_final: 0.8060 (ptt90) REVERT: A 990 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8263 (mm-30) REVERT: A 1067 TYR cc_start: 0.7978 (t80) cc_final: 0.7682 (t80) REVERT: A 1113 GLN cc_start: 0.8730 (mt0) cc_final: 0.8494 (mt0) REVERT: B 104 TRP cc_start: 0.6627 (m-90) cc_final: 0.6267 (m-90) REVERT: B 153 MET cc_start: 0.7768 (mtm) cc_final: 0.7003 (tpt) REVERT: B 378 LYS cc_start: 0.6500 (mmtt) cc_final: 0.6080 (mmmt) REVERT: B 524 VAL cc_start: 0.8305 (t) cc_final: 0.7930 (p) REVERT: B 542 ASN cc_start: 0.7715 (m-40) cc_final: 0.6749 (t0) REVERT: B 563 GLN cc_start: 0.7319 (mt0) cc_final: 0.6506 (mp10) REVERT: B 726 ILE cc_start: 0.7776 (pt) cc_final: 0.7434 (pt) REVERT: B 727 LEU cc_start: 0.8873 (mt) cc_final: 0.8493 (mt) REVERT: B 737 ASP cc_start: 0.8241 (p0) cc_final: 0.7722 (p0) REVERT: B 740 MET cc_start: 0.8403 (ttp) cc_final: 0.8115 (ttt) REVERT: B 764 ASN cc_start: 0.8803 (m110) cc_final: 0.8583 (m110) REVERT: B 773 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8813 (tp30) REVERT: B 776 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8886 (tmmt) REVERT: B 861 LEU cc_start: 0.9610 (tt) cc_final: 0.9324 (tt) REVERT: B 904 TYR cc_start: 0.8372 (t80) cc_final: 0.7771 (t80) REVERT: B 949 GLN cc_start: 0.8285 (tp40) cc_final: 0.8041 (tp-100) REVERT: B 1038 LYS cc_start: 0.8848 (mptt) cc_final: 0.8609 (mmtt) REVERT: B 1052 PHE cc_start: 0.8463 (m-10) cc_final: 0.8177 (m-10) REVERT: B 1095 PHE cc_start: 0.8093 (m-10) cc_final: 0.7026 (m-10) REVERT: B 1110 TYR cc_start: 0.8077 (t80) cc_final: 0.7740 (t80) REVERT: C 58 PHE cc_start: 0.7148 (m-80) cc_final: 0.6419 (m-80) REVERT: C 314 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9082 (tm-30) REVERT: C 453 TYR cc_start: 0.8111 (p90) cc_final: 0.7316 (p90) REVERT: C 761 THR cc_start: 0.8540 (p) cc_final: 0.8320 (p) REVERT: C 865 LEU cc_start: 0.9678 (mt) cc_final: 0.9471 (mt) REVERT: C 878 LEU cc_start: 0.9421 (mt) cc_final: 0.9217 (mt) REVERT: C 909 ILE cc_start: 0.8626 (mm) cc_final: 0.8416 (mm) REVERT: C 919 ASN cc_start: 0.9508 (t0) cc_final: 0.9190 (t0) REVERT: C 923 ILE cc_start: 0.9452 (mt) cc_final: 0.8546 (mt) REVERT: C 925 ASN cc_start: 0.9327 (t0) cc_final: 0.8926 (t0) REVERT: C 961 THR cc_start: 0.9315 (p) cc_final: 0.9063 (p) REVERT: C 1010 GLN cc_start: 0.8760 (pm20) cc_final: 0.8543 (pm20) REVERT: C 1019 ARG cc_start: 0.9157 (mtp-110) cc_final: 0.8846 (ptm160) REVERT: C 1028 LYS cc_start: 0.8460 (mttt) cc_final: 0.8118 (mttm) REVERT: C 1109 PHE cc_start: 0.8910 (t80) cc_final: 0.8619 (t80) REVERT: C 1111 GLU cc_start: 0.8184 (tp30) cc_final: 0.7691 (tp30) REVERT: C 1113 GLN cc_start: 0.8174 (mp10) cc_final: 0.6894 (mp10) outliers start: 1 outliers final: 1 residues processed: 649 average time/residue: 0.3267 time to fit residues: 332.0480 Evaluate side-chains 548 residues out of total 2672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 547 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 784 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 87 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1054 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145405 restraints weight = 54539.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149462 restraints weight = 33001.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152233 restraints weight = 22291.351| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24570 Z= 0.221 Angle : 0.736 12.391 33483 Z= 0.365 Chirality : 0.049 0.407 4035 Planarity : 0.005 0.086 4250 Dihedral : 8.540 100.276 4401 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.18 % Favored : 87.76 % Rotamer: Outliers : 0.08 % Allowed : 0.32 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.14), residues: 3006 helix: -0.07 (0.20), residues: 623 sheet: -1.77 (0.25), residues: 416 loop : -2.92 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.006 0.001 HIS C1058 PHE 0.038 0.002 PHE B 559 TYR 0.022 0.002 TYR C 170 ARG 0.008 0.001 ARG C 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6233.75 seconds wall clock time: 113 minutes 4.85 seconds (6784.85 seconds total)