Starting phenix.real_space_refine on Mon Jun 23 11:40:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k47_36879/06_2025/8k47_36879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k47_36879/06_2025/8k47_36879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k47_36879/06_2025/8k47_36879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k47_36879/06_2025/8k47_36879.map" model { file = "/net/cci-nas-00/data/ceres_data/8k47_36879/06_2025/8k47_36879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k47_36879/06_2025/8k47_36879.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 17153 2.51 5 N 4385 2.21 5 O 5262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26919 Number of models: 1 Model: "" Number of chains: 20 Chain: "I" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Conformer: "B" Number of residues, atoms: 124, 981 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} bond proxies already assigned to first conformer: 1003 Chain: "A" Number of atoms: 8385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8385 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 57, 'TRANS': 1027} Chain breaks: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 8410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8410 Classifications: {'peptide': 1084} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 8437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8437 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "J" 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: 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER I 26 " occ=0.37 ... (10 atoms not shown) pdb=" OG BSER I 26 " occ=0.63 Time building chain proxies: 18.31, per 1000 atoms: 0.68 Number of scatterers: 26919 At special positions: 0 Unit cell: (139.536, 154.224, 197.472, 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 119 16.00 O 5262 8.00 N 4385 7.00 C 17153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 164 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG J 1 " - " ASN C 343 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 801 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C1134 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG X 1 " - " ASN A 717 " " NAG Y 1 " - " ASN A 801 " " NAG Z 1 " - " ASN A1098 " " NAG a 1 " - " ASN A1134 " Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 3.6 seconds 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 54 sheets defined 22.7% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.568A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.747A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.960A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.606A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.655A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.999A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.533A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.846A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.098A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.559A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.533A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.887A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1150 removed outlier: 4.215A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.176A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 543 through 546 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.635A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.056A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 4.306A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.958A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.695A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.105A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.902A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.667A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.597A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.096A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.906A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.541A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.016A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.233A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.884A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.506A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.743A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1150 removed outlier: 4.230A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 2 through 8 removed outlier: 3.535A pdb=" N ALA I 2 " --> pdb=" O TRP I 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP I 28 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU I 82 " --> pdb=" O LEU I 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 2 through 8 removed outlier: 3.535A pdb=" N ALA I 2 " --> pdb=" O TRP I 28 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP I 28 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 375 " --> pdb=" O GLY I 27 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA I 29 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.169A pdb=" N TRP I 37 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA I 51 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N MET I 35 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP I 100 " --> pdb=" O HIS I 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AA6, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.515A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.530A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.801A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AB3, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AB4, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AB5, first strand: chain 'A' and resid 310 through 318 removed outlier: 5.277A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.702A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB8, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AB9, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AC2, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.069A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.069A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.192A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.386A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.597A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.547A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.544A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 276 through 279 removed outlier: 3.703A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 310 through 318 removed outlier: 7.230A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 326 through 327 removed outlier: 3.533A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AD6, first strand: chain 'B' and resid 400 through 403 removed outlier: 3.524A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.504A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 719 removed outlier: 6.788A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.069A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AE3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AE4, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.580A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE8, first strand: chain 'C' and resid 225 through 229 removed outlier: 5.947A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 309 through 318 removed outlier: 6.188A pdb=" N GLU C 309 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY C 601 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.588A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 378 through 380 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF5, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.870A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.870A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 734 removed outlier: 3.949A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.508A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 847 hydrogen bonds defined for protein. 2295 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: 10.32 Time building geometry restraints manager: 9.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4674 1.32 - 1.45: 7787 1.45 - 1.58: 14943 1.58 - 1.71: 0 1.71 - 1.84: 152 Bond restraints: 27556 Sorted by residual: bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.457 1.484 -0.027 6.40e-03 2.44e+04 1.84e+01 bond pdb=" CA SER A 708 " pdb=" CB SER A 708 " ideal model delta sigma weight residual 1.535 1.478 0.057 1.32e-02 5.74e+03 1.84e+01 bond pdb=" CA SER C1097 " pdb=" CB SER C1097 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.50e-02 4.44e+03 1.35e+01 bond pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N CYS B 131 " pdb=" CA CYS B 131 " ideal model delta sigma weight residual 1.457 1.503 -0.045 1.29e-02 6.01e+03 1.24e+01 ... (remaining 27551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 36792 2.96 - 5.92: 718 5.92 - 8.88: 30 8.88 - 11.84: 7 11.84 - 14.80: 2 Bond angle restraints: 37549 Sorted by residual: angle pdb=" C CYS B 361 " pdb=" CA CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sigma weight residual 114.40 102.34 12.06 1.25e+00 6.40e-01 9.31e+01 angle pdb=" N VAL B 159 " pdb=" CA VAL B 159 " pdb=" C VAL B 159 " ideal model delta sigma weight residual 110.23 102.13 8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" O GLY A 107 " ideal model delta sigma weight residual 122.45 117.68 4.77 7.20e-01 1.93e+00 4.38e+01 angle pdb=" N TRP B 64 " pdb=" CA TRP B 64 " pdb=" C TRP B 64 " ideal model delta sigma weight residual 113.19 105.49 7.70 1.19e+00 7.06e-01 4.18e+01 angle pdb=" N ASN B 542 " pdb=" CA ASN B 542 " pdb=" C ASN B 542 " ideal model delta sigma weight residual 112.41 105.36 7.05 1.30e+00 5.92e-01 2.94e+01 ... (remaining 37544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 15093 23.88 - 47.75: 1509 47.75 - 71.63: 284 71.63 - 95.50: 57 95.50 - 119.38: 31 Dihedral angle restraints: 16974 sinusoidal: 7142 harmonic: 9832 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 174.21 -81.21 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -11.84 -74.16 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 19.42 73.58 1 1.00e+01 1.00e-02 6.89e+01 ... (remaining 16971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 4307 0.177 - 0.354: 61 0.354 - 0.531: 11 0.531 - 0.708: 1 0.708 - 0.885: 3 Chirality restraints: 4383 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.50e+03 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.74e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.29e+01 ... (remaining 4380 not shown) Planarity restraints: 4839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.356 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG B1302 " 0.092 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG C1306 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.523 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " -0.335 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG C1307 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.164 2.00e-02 2.50e+03 ... (remaining 4836 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2254 2.73 - 3.27: 28432 3.27 - 3.81: 47233 3.81 - 4.36: 55322 4.36 - 4.90: 91853 Nonbonded interactions: 225094 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OD1 ASN A 394 " model vdw 2.184 3.040 nonbonded pdb=" O SER I 1 " pdb=" OH TYR I 113 " model vdw 2.202 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.207 3.040 nonbonded pdb=" O ARG C 634 " pdb=" OG SER C 637 " model vdw 2.212 3.040 ... (remaining 225089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 67 or resid 72 through 131 or (resid 132 throug \ h 134 and (name N or name CA or name C or name O or name CB )) or resid 135 thro \ ugh 327 or (resid 328 and (name N or name CA or name C or name O or name CB )) o \ r resid 329 or (resid 330 through 332 and (name N or name CA or name C or name O \ or name CB )) or resid 333 through 345 or (resid 346 and (name N or name CA or \ name C or name O or name CB )) or resid 347 through 354 or (resid 355 and (name \ N or name CA or name C or name O or name CB )) or resid 356 through 465 or (resi \ d 466 and (name N or name CA or name C or name O or name CB )) or resid 467 thro \ ugh 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) o \ r resid 510 through 525 or resid 530 through 577 or (resid 578 and (name N or na \ me CA or name C or name O or name CB )) or resid 579 through 1150 or resid 1301 \ through 1308)) selection = (chain 'B' and (resid 29 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 67 or resi \ d 72 through 133 or (resid 134 and (name N or name CA or name C or name O or nam \ e CB )) or resid 135 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 through 329 or (resid 330 through 332 and ( \ name N or name CA or name C or name O or name CB )) or resid 333 through 337 or \ (resid 338 and (name N or name CA or name C or name O or name CB )) or resid 339 \ or (resid 340 and (name N or name CA or name C or name O or name CB )) or resid \ 341 through 465 or (resid 466 and (name N or name CA or name C or name O or nam \ e CB )) or resid 467 through 508 or (resid 509 and (name N or name CA or name C \ or name O or name CB )) or resid 510 through 536 or (resid 537 and (name N or na \ me CA or name C or name O or name CB )) or resid 538 through 557 or (resid 558 a \ nd (name N or name CA or name C or name O or name CB )) or resid 559 through 577 \ or (resid 578 and (name N or name CA or name C or name O or name CB )) or resid \ 579 or (resid 580 and (name N or name CA or name C or name O or name CB )) or r \ esid 581 through 853 or (resid 854 through 855 and (name N or name CA or name C \ or name O or name CB )) or resid 856 through 1150 or resid 1301 through 1308)) selection = (chain 'C' and (resid 29 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 42 or (resid 43 through 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 through 46 or (res \ id 47 and (name N or name CA or name C or name O or name CB )) or resid 48 throu \ gh 67 or resid 72 through 131 or (resid 132 through 134 and (name N or name CA o \ r name C or name O or name CB )) or resid 135 through 236 or (resid 237 and (nam \ e N or name CA or name C or name O or name CB )) or resid 238 through 257 or (re \ sid 258 and (name N or name CA or name C or name O or name CB )) or resid 259 th \ rough 327 or (resid 328 and (name N or name CA or name C or name O or name CB )) \ or resid 329 through 331 or (resid 332 and (name N or name CA or name C or name \ O or name CB )) or resid 333 through 337 or (resid 338 and (name N or name CA o \ r name C or name O or name CB )) or resid 339 or (resid 340 and (name N or name \ CA or name C or name O or name CB )) or resid 341 through 525 or resid 530 throu \ gh 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) or \ resid 538 through 557 or (resid 558 and (name N or name CA or name C or name O \ or name CB )) or resid 559 through 579 or (resid 580 and (name N or name CA or n \ ame C or name O or name CB )) or resid 581 through 853 or (resid 854 through 855 \ and (name N or name CA or name C or name O or name CB )) or resid 856 through 1 \ 150 or resid 1301 through 1308)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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=0.37 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: 7.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 64.750 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.006 0.057 27641 Z= 0.383 Angle : 0.928 14.803 37767 Z= 0.560 Chirality : 0.066 0.885 4383 Planarity : 0.018 0.305 4804 Dihedral : 19.115 119.379 10551 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 1.52 % Allowed : 9.44 % Favored : 89.03 % Rotamer: Outliers : 5.01 % Allowed : 28.36 % Favored : 66.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 3350 helix: 1.31 (0.21), residues: 692 sheet: -1.79 (0.21), residues: 529 loop : -2.27 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 633 HIS 0.011 0.001 HIS C 207 PHE 0.063 0.002 PHE B 377 TYR 0.023 0.001 TYR B 636 ARG 0.008 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00996 ( 35) link_NAG-ASN : angle 3.43391 ( 105) link_BETA1-4 : bond 0.00499 ( 13) link_BETA1-4 : angle 2.55775 ( 39) hydrogen bonds : bond 0.21111 ( 827) hydrogen bonds : angle 9.03890 ( 2295) SS BOND : bond 0.00570 ( 37) SS BOND : angle 1.85530 ( 74) covalent geometry : bond 0.00629 (27556) covalent geometry : angle 0.90563 (37549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 147 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6172 (tt) REVERT: A 161 SER cc_start: 0.4456 (OUTLIER) cc_final: 0.4232 (p) REVERT: A 177 MET cc_start: 0.6973 (mtp) cc_final: 0.6525 (mmt) REVERT: A 869 MET cc_start: 0.8694 (ptp) cc_final: 0.8433 (mtm) REVERT: B 101 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 111 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6418 (t0) REVERT: B 130 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7845 (t) REVERT: B 377 PHE cc_start: -0.0489 (OUTLIER) cc_final: -0.0727 (m-10) REVERT: C 234 ASN cc_start: 0.4386 (OUTLIER) cc_final: 0.3818 (t0) outliers start: 145 outliers final: 38 residues processed: 281 average time/residue: 0.3388 time to fit residues: 157.8391 Evaluate side-chains 179 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 10.0000 chunk 254 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 86 optimal weight: 0.4980 chunk 171 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 59 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 165 ASN A 334 ASN A 532 ASN A1119 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 121 ASN C 370 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.116150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.075561 restraints weight = 131420.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.078965 restraints weight = 52547.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079378 restraints weight = 28774.537| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27641 Z= 0.227 Angle : 0.757 12.207 37767 Z= 0.371 Chirality : 0.048 0.346 4383 Planarity : 0.005 0.078 4804 Dihedral : 11.890 101.118 4744 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.26 % Favored : 90.44 % Rotamer: Outliers : 4.49 % Allowed : 27.70 % Favored : 67.81 % 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: -1.96 (0.14), residues: 3350 helix: 1.41 (0.21), residues: 688 sheet: -1.79 (0.20), residues: 565 loop : -2.24 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.004 0.001 HIS A 207 PHE 0.034 0.002 PHE C 157 TYR 0.030 0.002 TYR C 365 ARG 0.005 0.001 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 35) link_NAG-ASN : angle 3.09401 ( 105) link_BETA1-4 : bond 0.00578 ( 13) link_BETA1-4 : angle 2.31018 ( 39) hydrogen bonds : bond 0.04717 ( 827) hydrogen bonds : angle 6.83426 ( 2295) SS BOND : bond 0.00734 ( 37) SS BOND : angle 1.88603 ( 74) covalent geometry : bond 0.00503 (27556) covalent geometry : angle 0.73240 (37549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 140 time to evaluate : 3.080 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: A 177 MET cc_start: 0.6892 (mtp) cc_final: 0.6382 (mmt) REVERT: A 247 SER cc_start: 0.4969 (OUTLIER) cc_final: 0.4674 (t) REVERT: A 250 THR cc_start: 0.4793 (OUTLIER) cc_final: 0.4289 (p) REVERT: A 393 THR cc_start: 0.2790 (OUTLIER) cc_final: 0.2234 (t) REVERT: A 534 VAL cc_start: 0.5444 (OUTLIER) cc_final: 0.4994 (m) REVERT: A 1002 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 117 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8848 (mp) REVERT: B 226 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7867 (mm) REVERT: B 377 PHE cc_start: -0.0050 (OUTLIER) cc_final: -0.0396 (m-10) REVERT: B 449 TYR cc_start: -0.0217 (OUTLIER) cc_final: -0.1252 (t80) REVERT: C 170 TYR cc_start: 0.8323 (t80) cc_final: 0.7862 (t80) REVERT: C 234 ASN cc_start: 0.4354 (OUTLIER) cc_final: 0.4048 (t0) REVERT: C 354 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8031 (p0) REVERT: C 773 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8070 (tm-30) outliers start: 130 outliers final: 58 residues processed: 258 average time/residue: 0.3631 time to fit residues: 161.2322 Evaluate side-chains 191 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 56 optimal weight: 20.0000 chunk 176 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 211 optimal weight: 0.8980 chunk 16 optimal weight: 40.0000 chunk 151 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 263 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.113138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.071294 restraints weight = 123172.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.073557 restraints weight = 49777.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.075001 restraints weight = 30051.765| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27641 Z= 0.149 Angle : 0.662 11.359 37767 Z= 0.325 Chirality : 0.046 0.254 4383 Planarity : 0.004 0.078 4804 Dihedral : 10.650 100.317 4714 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.92 % Favored : 91.78 % Rotamer: Outliers : 4.25 % Allowed : 27.98 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3350 helix: 1.49 (0.21), residues: 688 sheet: -1.82 (0.20), residues: 549 loop : -2.16 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 633 HIS 0.003 0.001 HIS C 207 PHE 0.037 0.002 PHE C 157 TYR 0.016 0.001 TYR B 904 ARG 0.004 0.000 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 35) link_NAG-ASN : angle 2.53280 ( 105) link_BETA1-4 : bond 0.00429 ( 13) link_BETA1-4 : angle 1.95033 ( 39) hydrogen bonds : bond 0.04188 ( 827) hydrogen bonds : angle 6.37258 ( 2295) SS BOND : bond 0.00444 ( 37) SS BOND : angle 1.69160 ( 74) covalent geometry : bond 0.00337 (27556) covalent geometry : angle 0.64262 (37549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 141 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6812 (mtp) cc_final: 0.6307 (mmt) REVERT: A 204 TYR cc_start: 0.8402 (m-80) cc_final: 0.7995 (m-80) REVERT: A 223 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7748 (tp) REVERT: A 247 SER cc_start: 0.4265 (OUTLIER) cc_final: 0.3729 (t) REVERT: A 250 THR cc_start: 0.4665 (OUTLIER) cc_final: 0.4260 (p) REVERT: A 393 THR cc_start: 0.3752 (OUTLIER) cc_final: 0.3311 (t) REVERT: A 534 VAL cc_start: 0.5489 (OUTLIER) cc_final: 0.5117 (m) REVERT: A 878 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9152 (mt) REVERT: A 1002 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 117 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 153 MET cc_start: 0.3951 (ptt) cc_final: 0.3699 (tmm) REVERT: B 226 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7906 (mm) REVERT: B 377 PHE cc_start: 0.1970 (OUTLIER) cc_final: 0.1064 (m-10) REVERT: B 449 TYR cc_start: 0.0007 (OUTLIER) cc_final: -0.0469 (t80) REVERT: B 1028 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8496 (ptmt) REVERT: C 45 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8274 (t) REVERT: C 170 TYR cc_start: 0.8351 (t80) cc_final: 0.7825 (t80) REVERT: C 234 ASN cc_start: 0.4443 (OUTLIER) cc_final: 0.4166 (t0) REVERT: C 354 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7890 (p0) REVERT: C 365 TYR cc_start: 0.7079 (t80) cc_final: 0.6743 (t80) REVERT: C 370 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7155 (p0) REVERT: C 371 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6501 (t80) REVERT: C 495 TYR cc_start: 0.3408 (OUTLIER) cc_final: 0.2991 (m-80) REVERT: C 773 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7935 (tm-30) outliers start: 123 outliers final: 54 residues processed: 251 average time/residue: 0.3528 time to fit residues: 151.8841 Evaluate side-chains 200 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 78 optimal weight: 0.6980 chunk 329 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 0.0770 chunk 125 optimal weight: 0.0010 chunk 327 optimal weight: 0.7980 chunk 129 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 199 optimal weight: 0.0020 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN C 196 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.113460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070990 restraints weight = 125541.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073454 restraints weight = 49972.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.074850 restraints weight = 29705.945| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 27641 Z= 0.114 Angle : 0.645 14.256 37767 Z= 0.312 Chirality : 0.045 0.407 4383 Planarity : 0.004 0.078 4804 Dihedral : 9.511 97.753 4704 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.01 % Favored : 91.69 % Rotamer: Outliers : 3.77 % Allowed : 28.05 % Favored : 68.19 % 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: -1.69 (0.14), residues: 3350 helix: 1.58 (0.21), residues: 695 sheet: -1.58 (0.20), residues: 549 loop : -2.06 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.002 0.001 HIS C1088 PHE 0.041 0.001 PHE C 157 TYR 0.016 0.001 TYR C 369 ARG 0.004 0.000 ARG I 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 35) link_NAG-ASN : angle 2.72961 ( 105) link_BETA1-4 : bond 0.00603 ( 13) link_BETA1-4 : angle 1.69389 ( 39) hydrogen bonds : bond 0.03700 ( 827) hydrogen bonds : angle 5.91776 ( 2295) SS BOND : bond 0.00354 ( 37) SS BOND : angle 1.58864 ( 74) covalent geometry : bond 0.00253 (27556) covalent geometry : angle 0.62431 (37549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 148 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 74 ASP cc_start: 0.7669 (t70) cc_final: 0.7398 (p0) REVERT: A 177 MET cc_start: 0.6980 (mtp) cc_final: 0.6424 (mmt) REVERT: A 200 TYR cc_start: 0.9046 (m-80) cc_final: 0.8681 (t80) REVERT: A 204 TYR cc_start: 0.8382 (m-80) cc_final: 0.8072 (m-80) REVERT: A 247 SER cc_start: 0.4484 (OUTLIER) cc_final: 0.4045 (t) REVERT: A 250 THR cc_start: 0.4757 (OUTLIER) cc_final: 0.4474 (p) REVERT: A 393 THR cc_start: 0.3727 (OUTLIER) cc_final: 0.3264 (t) REVERT: A 534 VAL cc_start: 0.5380 (OUTLIER) cc_final: 0.5061 (m) REVERT: A 878 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9136 (mt) REVERT: A 939 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8807 (t) REVERT: A 1002 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 140 PHE cc_start: 0.2142 (OUTLIER) cc_final: 0.1272 (m-80) REVERT: B 377 PHE cc_start: 0.1419 (OUTLIER) cc_final: 0.0558 (m-10) REVERT: B 449 TYR cc_start: 0.0027 (OUTLIER) cc_final: -0.0524 (t80) REVERT: C 45 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8282 (t) REVERT: C 146 HIS cc_start: 0.4758 (OUTLIER) cc_final: 0.3806 (p90) REVERT: C 170 TYR cc_start: 0.8341 (t80) cc_final: 0.7868 (t80) REVERT: C 354 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7868 (p0) REVERT: C 365 TYR cc_start: 0.6836 (t80) cc_final: 0.6508 (t80) REVERT: C 370 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.6981 (p0) REVERT: C 371 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6430 (t80) REVERT: C 495 TYR cc_start: 0.3308 (OUTLIER) cc_final: 0.2973 (m-80) REVERT: C 516 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7264 (pp20) REVERT: C 773 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7757 (tm-30) outliers start: 109 outliers final: 46 residues processed: 244 average time/residue: 0.3671 time to fit residues: 153.5194 Evaluate side-chains 194 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 2.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 61 optimal weight: 20.0000 chunk 331 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 332 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 258 optimal weight: 20.0000 chunk 277 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1005 GLN B1135 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.112238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.073581 restraints weight = 152141.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076210 restraints weight = 59148.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076513 restraints weight = 29766.396| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27641 Z= 0.202 Angle : 0.681 23.550 37767 Z= 0.331 Chirality : 0.046 0.672 4383 Planarity : 0.004 0.077 4804 Dihedral : 9.038 98.699 4689 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.80 % Favored : 91.90 % Rotamer: Outliers : 4.11 % Allowed : 27.77 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3350 helix: 1.63 (0.21), residues: 687 sheet: -1.54 (0.20), residues: 567 loop : -2.10 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 633 HIS 0.004 0.001 HIS C1064 PHE 0.038 0.002 PHE C 157 TYR 0.015 0.001 TYR C1067 ARG 0.018 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 35) link_NAG-ASN : angle 3.62023 ( 105) link_BETA1-4 : bond 0.00459 ( 13) link_BETA1-4 : angle 1.65062 ( 39) hydrogen bonds : bond 0.03917 ( 827) hydrogen bonds : angle 5.89722 ( 2295) SS BOND : bond 0.00460 ( 37) SS BOND : angle 1.78095 ( 74) covalent geometry : bond 0.00453 (27556) covalent geometry : angle 0.64914 (37549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 138 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 48 PHE cc_start: 0.3306 (OUTLIER) cc_final: 0.2761 (t80) REVERT: A 64 TRP cc_start: 0.7919 (t-100) cc_final: 0.7486 (t-100) REVERT: A 177 MET cc_start: 0.7002 (mtp) cc_final: 0.6492 (mmt) REVERT: A 200 TYR cc_start: 0.9064 (m-80) cc_final: 0.8686 (t80) REVERT: A 393 THR cc_start: 0.2496 (OUTLIER) cc_final: 0.1859 (t) REVERT: A 534 VAL cc_start: 0.5452 (OUTLIER) cc_final: 0.5055 (m) REVERT: A 878 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9129 (mt) REVERT: A 1002 GLN cc_start: 0.8531 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 226 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7876 (mm) REVERT: B 449 TYR cc_start: 0.0194 (OUTLIER) cc_final: -0.1029 (t80) REVERT: B 1028 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8660 (ptmt) REVERT: C 45 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8426 (t) REVERT: C 170 TYR cc_start: 0.8460 (t80) cc_final: 0.7908 (t80) REVERT: C 177 MET cc_start: 0.8508 (ptt) cc_final: 0.8240 (tpp) REVERT: C 365 TYR cc_start: 0.7184 (t80) cc_final: 0.6643 (t80) REVERT: C 370 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7026 (p0) REVERT: C 371 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6319 (t80) REVERT: C 495 TYR cc_start: 0.3675 (OUTLIER) cc_final: 0.3208 (m-80) REVERT: C 1031 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7275 (mp0) outliers start: 118 outliers final: 78 residues processed: 242 average time/residue: 0.4134 time to fit residues: 173.1261 Evaluate side-chains 219 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 129 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 224 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 260 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 21 optimal weight: 0.0870 chunk 163 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.113029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071105 restraints weight = 134095.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.073518 restraints weight = 52431.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.075078 restraints weight = 30738.358| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27641 Z= 0.140 Angle : 0.640 18.954 37767 Z= 0.310 Chirality : 0.045 0.569 4383 Planarity : 0.004 0.075 4804 Dihedral : 8.633 97.065 4686 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.01 % Favored : 91.69 % Rotamer: Outliers : 3.80 % Allowed : 28.36 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3350 helix: 1.72 (0.21), residues: 679 sheet: -1.46 (0.20), residues: 569 loop : -2.05 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.003 0.001 HIS C 207 PHE 0.036 0.001 PHE C 157 TYR 0.017 0.001 TYR B1138 ARG 0.011 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 35) link_NAG-ASN : angle 3.30855 ( 105) link_BETA1-4 : bond 0.00447 ( 13) link_BETA1-4 : angle 1.57670 ( 39) hydrogen bonds : bond 0.03730 ( 827) hydrogen bonds : angle 5.78159 ( 2295) SS BOND : bond 0.00421 ( 37) SS BOND : angle 1.55235 ( 74) covalent geometry : bond 0.00315 (27556) covalent geometry : angle 0.61117 (37549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 134 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 48 PHE cc_start: 0.2053 (OUTLIER) cc_final: 0.1761 (t80) REVERT: A 64 TRP cc_start: 0.7664 (t-100) cc_final: 0.7397 (t-100) REVERT: A 177 MET cc_start: 0.6984 (mtp) cc_final: 0.6431 (mmt) REVERT: A 200 TYR cc_start: 0.9077 (m-80) cc_final: 0.8722 (t80) REVERT: A 204 TYR cc_start: 0.8559 (m-80) cc_final: 0.7991 (m-80) REVERT: A 247 SER cc_start: 0.4278 (OUTLIER) cc_final: 0.3724 (t) REVERT: A 393 THR cc_start: 0.3576 (OUTLIER) cc_final: 0.3144 (t) REVERT: A 534 VAL cc_start: 0.5471 (OUTLIER) cc_final: 0.5146 (m) REVERT: A 869 MET cc_start: 0.8781 (ptp) cc_final: 0.8519 (mtm) REVERT: A 878 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9158 (mt) REVERT: A 1002 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 140 PHE cc_start: 0.2410 (OUTLIER) cc_final: 0.1520 (m-80) REVERT: B 449 TYR cc_start: 0.0022 (OUTLIER) cc_final: -0.0463 (t80) REVERT: B 1028 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8561 (ptmt) REVERT: C 45 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8415 (t) REVERT: C 170 TYR cc_start: 0.8508 (t80) cc_final: 0.8016 (t80) REVERT: C 365 TYR cc_start: 0.6991 (t80) cc_final: 0.6539 (t80) REVERT: C 370 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7191 (p0) REVERT: C 371 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6421 (t80) REVERT: C 495 TYR cc_start: 0.3565 (OUTLIER) cc_final: 0.3217 (m-80) REVERT: C 1002 GLN cc_start: 0.8275 (tp-100) cc_final: 0.8068 (tp40) REVERT: C 1031 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7286 (mp0) outliers start: 109 outliers final: 65 residues processed: 235 average time/residue: 0.4500 time to fit residues: 186.4753 Evaluate side-chains 208 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 130 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 282 optimal weight: 0.0370 chunk 239 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 150 optimal weight: 0.0270 chunk 178 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.113054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.073024 restraints weight = 146010.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.076738 restraints weight = 61128.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076083 restraints weight = 31103.430| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27641 Z= 0.111 Angle : 0.625 19.134 37767 Z= 0.301 Chirality : 0.044 0.498 4383 Planarity : 0.004 0.068 4804 Dihedral : 8.157 95.866 4686 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.35 % Favored : 92.41 % Rotamer: Outliers : 3.18 % Allowed : 28.53 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3350 helix: 1.81 (0.21), residues: 680 sheet: -1.38 (0.20), residues: 573 loop : -1.96 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.002 0.000 HIS C 207 PHE 0.037 0.001 PHE C 157 TYR 0.015 0.001 TYR C 369 ARG 0.008 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 35) link_NAG-ASN : angle 3.12345 ( 105) link_BETA1-4 : bond 0.00500 ( 13) link_BETA1-4 : angle 1.51616 ( 39) hydrogen bonds : bond 0.03455 ( 827) hydrogen bonds : angle 5.54627 ( 2295) SS BOND : bond 0.00370 ( 37) SS BOND : angle 1.76026 ( 74) covalent geometry : bond 0.00245 (27556) covalent geometry : angle 0.59772 (37549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 142 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 48 PHE cc_start: 0.2784 (OUTLIER) cc_final: 0.2476 (t80) REVERT: A 64 TRP cc_start: 0.8057 (t-100) cc_final: 0.7739 (t-100) REVERT: A 177 MET cc_start: 0.6985 (mtp) cc_final: 0.6457 (mmt) REVERT: A 200 TYR cc_start: 0.9134 (m-80) cc_final: 0.8757 (t80) REVERT: A 204 TYR cc_start: 0.8525 (m-80) cc_final: 0.8000 (m-80) REVERT: A 247 SER cc_start: 0.4832 (OUTLIER) cc_final: 0.4476 (t) REVERT: A 393 THR cc_start: 0.3097 (OUTLIER) cc_final: 0.2491 (t) REVERT: A 534 VAL cc_start: 0.5316 (OUTLIER) cc_final: 0.5105 (p) REVERT: A 780 GLU cc_start: 0.8413 (tp30) cc_final: 0.8189 (tp30) REVERT: A 869 MET cc_start: 0.8761 (ptp) cc_final: 0.8536 (mtm) REVERT: A 878 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9088 (mt) REVERT: A 1002 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 140 PHE cc_start: 0.1682 (OUTLIER) cc_final: 0.1072 (m-80) REVERT: B 449 TYR cc_start: 0.0038 (OUTLIER) cc_final: -0.1040 (t80) REVERT: B 559 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7369 (t80) REVERT: B 1028 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8364 (ptmt) REVERT: C 45 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8435 (t) REVERT: C 62 VAL cc_start: 0.7677 (m) cc_final: 0.7461 (p) REVERT: C 73 THR cc_start: 0.3056 (OUTLIER) cc_final: 0.2774 (p) REVERT: C 170 TYR cc_start: 0.8530 (t80) cc_final: 0.8055 (t80) REVERT: C 365 TYR cc_start: 0.6861 (t80) cc_final: 0.6327 (t80) REVERT: C 370 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7519 (p0) REVERT: C 371 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6371 (t80) REVERT: C 495 TYR cc_start: 0.3608 (OUTLIER) cc_final: 0.3241 (m-80) REVERT: C 739 THR cc_start: 0.8927 (m) cc_final: 0.8605 (t) REVERT: C 1005 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: C 1031 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7384 (mp0) outliers start: 90 outliers final: 58 residues processed: 224 average time/residue: 0.3712 time to fit residues: 143.9666 Evaluate side-chains 203 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 129 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 205 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 288 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 158 optimal weight: 30.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.111728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069393 restraints weight = 126952.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071737 restraints weight = 51193.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073096 restraints weight = 30621.098| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27641 Z= 0.206 Angle : 0.667 18.498 37767 Z= 0.325 Chirality : 0.045 0.515 4383 Planarity : 0.004 0.070 4804 Dihedral : 8.046 98.903 4686 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.31 % Favored : 91.48 % Rotamer: Outliers : 3.63 % Allowed : 28.01 % Favored : 68.36 % 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: -1.62 (0.14), residues: 3350 helix: 1.68 (0.20), residues: 684 sheet: -1.51 (0.20), residues: 585 loop : -2.02 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.004 0.001 HIS C 245 PHE 0.036 0.002 PHE C 157 TYR 0.015 0.001 TYR A1067 ARG 0.008 0.001 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 35) link_NAG-ASN : angle 3.19778 ( 105) link_BETA1-4 : bond 0.00372 ( 13) link_BETA1-4 : angle 1.58138 ( 39) hydrogen bonds : bond 0.03861 ( 827) hydrogen bonds : angle 5.69250 ( 2295) SS BOND : bond 0.00509 ( 37) SS BOND : angle 2.15807 ( 74) covalent geometry : bond 0.00462 (27556) covalent geometry : angle 0.63758 (37549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 131 time to evaluate : 2.863 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: I 48 PHE cc_start: 0.2487 (OUTLIER) cc_final: 0.2236 (t80) REVERT: A 177 MET cc_start: 0.6902 (mtp) cc_final: 0.6369 (mmt) REVERT: A 200 TYR cc_start: 0.9064 (m-80) cc_final: 0.8712 (t80) REVERT: A 247 SER cc_start: 0.4165 (OUTLIER) cc_final: 0.3649 (t) REVERT: A 393 THR cc_start: 0.3423 (OUTLIER) cc_final: 0.2919 (t) REVERT: A 534 VAL cc_start: 0.5464 (OUTLIER) cc_final: 0.5250 (p) REVERT: A 869 MET cc_start: 0.8802 (ptp) cc_final: 0.8596 (mtm) REVERT: A 1002 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 140 PHE cc_start: 0.2421 (OUTLIER) cc_final: 0.1674 (m-80) REVERT: B 224 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: B 449 TYR cc_start: 0.0103 (OUTLIER) cc_final: -0.0450 (t80) REVERT: B 611 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9104 (tp) REVERT: B 1028 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8647 (ptmt) REVERT: C 45 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 73 THR cc_start: 0.3925 (OUTLIER) cc_final: 0.3557 (p) REVERT: C 170 TYR cc_start: 0.8578 (t80) cc_final: 0.8058 (t80) REVERT: C 365 TYR cc_start: 0.7138 (t80) cc_final: 0.6495 (t80) REVERT: C 370 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7782 (p0) REVERT: C 371 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6074 (t80) REVERT: C 1002 GLN cc_start: 0.8526 (tp40) cc_final: 0.8325 (tp40) REVERT: C 1005 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: C 1031 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7313 (mp0) outliers start: 103 outliers final: 74 residues processed: 225 average time/residue: 0.3213 time to fit residues: 125.2971 Evaluate side-chains 211 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 122 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9990 chunk 273 optimal weight: 0.7980 chunk 282 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 0.0980 chunk 140 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.111869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069411 restraints weight = 129995.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071628 restraints weight = 53693.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.073120 restraints weight = 32934.035| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27641 Z= 0.122 Angle : 0.630 18.758 37767 Z= 0.304 Chirality : 0.044 0.489 4383 Planarity : 0.004 0.067 4804 Dihedral : 7.773 96.089 4686 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.71 % Favored : 92.08 % Rotamer: Outliers : 3.45 % Allowed : 28.70 % Favored : 67.84 % 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: -1.54 (0.14), residues: 3350 helix: 1.75 (0.21), residues: 682 sheet: -1.55 (0.20), residues: 593 loop : -1.93 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 633 HIS 0.004 0.001 HIS C 245 PHE 0.038 0.001 PHE C 157 TYR 0.014 0.001 TYR B 904 ARG 0.006 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 35) link_NAG-ASN : angle 3.06721 ( 105) link_BETA1-4 : bond 0.00447 ( 13) link_BETA1-4 : angle 1.48805 ( 39) hydrogen bonds : bond 0.03568 ( 827) hydrogen bonds : angle 5.53486 ( 2295) SS BOND : bond 0.00363 ( 37) SS BOND : angle 1.88844 ( 74) covalent geometry : bond 0.00275 (27556) covalent geometry : angle 0.60312 (37549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 127 time to evaluate : 3.527 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: A 177 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6391 (mmt) REVERT: A 200 TYR cc_start: 0.9036 (m-80) cc_final: 0.8678 (t80) REVERT: A 204 TYR cc_start: 0.8531 (m-80) cc_final: 0.7927 (m-80) REVERT: A 393 THR cc_start: 0.3827 (OUTLIER) cc_final: 0.3370 (t) REVERT: A 534 VAL cc_start: 0.5459 (OUTLIER) cc_final: 0.5237 (p) REVERT: A 869 MET cc_start: 0.8717 (ptp) cc_final: 0.8488 (mtm) REVERT: A 878 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9161 (mt) REVERT: A 1002 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 140 PHE cc_start: 0.2407 (OUTLIER) cc_final: 0.1632 (m-80) REVERT: B 224 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: B 449 TYR cc_start: 0.0112 (OUTLIER) cc_final: -0.0427 (t80) REVERT: B 776 LYS cc_start: 0.9003 (tmmt) cc_final: 0.8758 (tmmt) REVERT: B 1028 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8499 (ptmt) REVERT: C 45 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8478 (t) REVERT: C 62 VAL cc_start: 0.7580 (m) cc_final: 0.7348 (p) REVERT: C 73 THR cc_start: 0.3983 (OUTLIER) cc_final: 0.3599 (p) REVERT: C 170 TYR cc_start: 0.8589 (t80) cc_final: 0.8199 (t80) REVERT: C 365 TYR cc_start: 0.6804 (t80) cc_final: 0.6255 (t80) REVERT: C 370 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7753 (p0) REVERT: C 371 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.5985 (t80) REVERT: C 1005 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: C 1031 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7351 (mp0) outliers start: 98 outliers final: 69 residues processed: 215 average time/residue: 0.3493 time to fit residues: 130.7552 Evaluate side-chains 207 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 124 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 216 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 295 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 311 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1101 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.111617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.070111 restraints weight = 106546.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.072191 restraints weight = 48305.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073374 restraints weight = 30338.485| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27641 Z= 0.128 Angle : 0.622 18.222 37767 Z= 0.300 Chirality : 0.044 0.483 4383 Planarity : 0.004 0.065 4804 Dihedral : 7.519 96.309 4686 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.83 % Favored : 91.96 % Rotamer: Outliers : 2.83 % Allowed : 29.26 % Favored : 67.91 % 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: -1.51 (0.15), residues: 3350 helix: 1.76 (0.21), residues: 686 sheet: -1.54 (0.20), residues: 595 loop : -1.90 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 633 HIS 0.004 0.001 HIS C 245 PHE 0.037 0.001 PHE C 157 TYR 0.013 0.001 TYR C 369 ARG 0.006 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 35) link_NAG-ASN : angle 3.00764 ( 105) link_BETA1-4 : bond 0.00414 ( 13) link_BETA1-4 : angle 1.46488 ( 39) hydrogen bonds : bond 0.03477 ( 827) hydrogen bonds : angle 5.43521 ( 2295) SS BOND : bond 0.00380 ( 37) SS BOND : angle 1.87240 ( 74) covalent geometry : bond 0.00290 (27556) covalent geometry : angle 0.59546 (37549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6700 Ramachandran restraints generated. 3350 Oldfield, 0 Emsley, 3350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 130 time to evaluate : 2.893 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: A 177 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6382 (mmt) REVERT: A 200 TYR cc_start: 0.8985 (m-80) cc_final: 0.8642 (t80) REVERT: A 204 TYR cc_start: 0.8561 (m-80) cc_final: 0.7923 (m-80) REVERT: A 393 THR cc_start: 0.3806 (OUTLIER) cc_final: 0.3304 (t) REVERT: A 534 VAL cc_start: 0.5464 (OUTLIER) cc_final: 0.5237 (p) REVERT: A 869 MET cc_start: 0.8714 (ptp) cc_final: 0.8512 (mtm) REVERT: A 878 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9174 (mt) REVERT: A 1002 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 140 PHE cc_start: 0.2334 (OUTLIER) cc_final: 0.2026 (m-80) REVERT: B 224 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: B 776 LYS cc_start: 0.9038 (tmmt) cc_final: 0.8779 (tmmt) REVERT: B 1028 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8539 (ptmt) REVERT: C 62 VAL cc_start: 0.7540 (m) cc_final: 0.7297 (p) REVERT: C 73 THR cc_start: 0.3974 (OUTLIER) cc_final: 0.3637 (p) REVERT: C 170 TYR cc_start: 0.8607 (t80) cc_final: 0.8235 (t80) REVERT: C 201 PHE cc_start: 0.8476 (t80) cc_final: 0.8083 (t80) REVERT: C 365 TYR cc_start: 0.6797 (t80) cc_final: 0.6217 (t80) REVERT: C 370 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7712 (p0) REVERT: C 371 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.5892 (t80) REVERT: C 1005 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: C 1031 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7402 (mp0) outliers start: 80 outliers final: 63 residues processed: 202 average time/residue: 0.3251 time to fit residues: 113.9993 Evaluate side-chains 202 residues out of total 2942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 127 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 95 TYR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 199 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 243 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 236 optimal weight: 9.9990 chunk 233 optimal weight: 0.0870 chunk 320 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 110 optimal weight: 0.5980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 804 GLN B1005 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.112400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.070646 restraints weight = 106737.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.072940 restraints weight = 46336.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.074203 restraints weight = 28685.506| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27641 Z= 0.107 Angle : 0.614 18.118 37767 Z= 0.296 Chirality : 0.044 0.477 4383 Planarity : 0.004 0.062 4804 Dihedral : 7.317 93.776 4684 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.53 % Favored : 92.26 % Rotamer: Outliers : 2.73 % Allowed : 29.40 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3350 helix: 1.76 (0.21), residues: 683 sheet: -1.44 (0.20), residues: 589 loop : -1.86 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 633 HIS 0.004 0.001 HIS A 207 PHE 0.037 0.001 PHE C 157 TYR 0.015 0.001 TYR B 904 ARG 0.005 0.000 ARG B 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 35) link_NAG-ASN : angle 2.93450 ( 105) link_BETA1-4 : bond 0.00491 ( 13) link_BETA1-4 : angle 1.42186 ( 39) hydrogen bonds : bond 0.03345 ( 827) hydrogen bonds : angle 5.33588 ( 2295) SS BOND : bond 0.00305 ( 37) SS BOND : angle 1.73209 ( 74) covalent geometry : bond 0.00238 (27556) covalent geometry : angle 0.58879 (37549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13695.13 seconds wall clock time: 243 minutes 26.35 seconds (14606.35 seconds total)