Starting phenix.real_space_refine on Mon Jul 6 07:23:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.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 { model { file = "/net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrt_23499/07_2026/7lrt_23499.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 148 5.16 5 C 21214 2.51 5 N 5485 2.21 5 O 6618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33465 Number of models: 1 Model: "" Number of chains: 34 Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1636 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "A" Number of atoms: 8494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8494 Classifications: {'peptide': 1085} Link IDs: {'PTRANS': 58, 'TRANS': 1026} Chain breaks: 4 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 5 Chain: "C" Number of atoms: 8516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8516 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "b" 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 chiralities: 2 Chain: "c" 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 chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.41, per 1000 atoms: 0.22 Number of scatterers: 33465 At special positions: 0 Unit cell: (157.32, 162.45, 267.615, 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 148 16.00 O 6618 8.00 N 5485 7.00 C 21214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 100B" distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " 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=2.04 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 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA Y 3 " - " MAN Y 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 149 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 17 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 17 " " NAG I 1 " - " ASN F 96 " " NAG J 1 " - " ASN H 96 " " NAG K 1 " - " ASN D 96 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 709 " " NAG R 1 " - " ASN A 17 " " NAG S 1 " - " ASN A 343 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B 331 " " NAG Y 1 " - " ASN B 343 " " NAG Z 1 " - " ASN C 331 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C 343 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7750 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 78 sheets defined 18.9% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.714A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.821A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.531A pdb=" N GLN E 124 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 4.097A pdb=" N SER E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.778A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.734A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.899A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.640A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.592A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.804A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.236A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.759A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 removed outlier: 4.484A pdb=" N LEU A 945 " --> pdb=" O PRO A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 947 through 965 removed outlier: 3.725A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.758A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.457A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1149 removed outlier: 4.167A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.724A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 4.055A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.899A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.693A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.695A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.574A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.519A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.863A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.612A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.603A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.358A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1149 removed outlier: 4.307A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.789A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.803A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.921A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.876A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.637A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.743A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.898A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 906 through 910 removed outlier: 3.628A pdb=" N GLY C 910 " --> pdb=" O ASN C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.971A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.142A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.622A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.922A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.099A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.512A pdb=" N LEU F 82 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AA3, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AA4, first strand: chain 'F' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.249A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 20 through 22 Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 49 removed outlier: 6.756A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 85 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 5 removed outlier: 4.366A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 33 through 36 removed outlier: 3.816A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.565A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.605A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.067A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.137A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 181 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.137A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 177 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.090A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AC4, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.941A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 150 removed outlier: 4.165A pdb=" N LYS E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR E 197 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS E 194 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS E 207 " --> pdb=" O CYS E 194 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL E 196 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.599A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AC9, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AD1, first strand: chain 'A' and resid 133 through 140 removed outlier: 8.361A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.176A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AD3, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AD4, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AD5, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.542A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.616A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.800A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.538A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AE3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AE4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.173A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.776A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.176A pdb=" N ALA B 67 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AF2, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AF3, first strand: chain 'B' and resid 153 through 163 removed outlier: 6.700A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 10.992A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.493A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.712A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AF6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.944A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AF8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AF9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AG1, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AG2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.904A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.495A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AG6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.672A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AG8, first strand: chain 'C' and resid 29 through 30 Processing sheet with id=AG9, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.317A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.040A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.649A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 83 through 85 removed outlier: 14.487A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.169A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.700A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.045A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.815A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.946A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.180A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AH9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AI1, first strand: chain 'C' and resid 539 through 542 removed outlier: 4.065A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.161A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.823A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AI5, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AI6, first strand: chain 'C' and resid 1094 through 1097 1032 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.73 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10570 1.34 - 1.46: 8490 1.46 - 1.58: 14977 1.58 - 1.70: 0 1.70 - 1.83: 190 Bond restraints: 34227 Sorted by residual: bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.49e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.47e-02 4.63e+03 5.05e+00 bond pdb=" C1 BMA e 3 " pdb=" C2 BMA e 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 34222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 44994 1.68 - 3.35: 1332 3.35 - 5.03: 195 5.03 - 6.71: 57 6.71 - 8.39: 6 Bond angle restraints: 46584 Sorted by residual: angle pdb=" N VAL B 635 " pdb=" CA VAL B 635 " pdb=" C VAL B 635 " ideal model delta sigma weight residual 113.71 106.72 6.99 9.50e-01 1.11e+00 5.42e+01 angle pdb=" C PRO C 330 " pdb=" N ASN C 331 " pdb=" CA ASN C 331 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N ILE F 48 " pdb=" CA ILE F 48 " pdb=" C ILE F 48 " ideal model delta sigma weight residual 111.90 109.00 2.90 8.10e-01 1.52e+00 1.28e+01 angle pdb=" N THR A 236 " pdb=" CA THR A 236 " pdb=" C THR A 236 " ideal model delta sigma weight residual 114.75 110.87 3.88 1.26e+00 6.30e-01 9.46e+00 angle pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" N VAL A 503 " ideal model delta sigma weight residual 114.23 116.93 -2.70 8.80e-01 1.29e+00 9.43e+00 ... (remaining 46579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17869 17.95 - 35.89: 1554 35.89 - 53.84: 256 53.84 - 71.78: 49 71.78 - 89.73: 36 Dihedral angle restraints: 19764 sinusoidal: 7704 harmonic: 12060 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 179.47 -86.47 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 88 " pdb=" CB CYS G 88 " ideal model delta sinusoidal sigma weight residual 93.00 159.39 -66.39 1 1.00e+01 1.00e-02 5.76e+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 -86.00 -149.92 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 19761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5170 0.096 - 0.192: 318 0.192 - 0.288: 12 0.288 - 0.384: 1 0.384 - 0.481: 1 Chirality restraints: 5502 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 603 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 5499 not shown) Planarity restraints: 5951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO C 330 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 104 " -0.031 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP C 104 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP C 104 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 104 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 104 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 104 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 104 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 104 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 104 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 104 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.036 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN A 331 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.039 2.00e-02 2.50e+03 ... (remaining 5948 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1104 2.70 - 3.25: 32684 3.25 - 3.80: 49705 3.80 - 4.35: 61477 4.35 - 4.90: 104894 Nonbonded interactions: 249864 Sorted by model distance: nonbonded pdb=" OH TYR B 453 " pdb=" OE1 GLN B 493 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.175 3.040 nonbonded pdb=" OG SER A 438 " pdb=" O PRO A 507 " model vdw 2.177 3.040 nonbonded pdb=" O6 NAG U 1 " pdb=" O3 NAG U 2 " model vdw 2.189 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.210 3.040 ... (remaining 249859 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 14 through 1307) selection = (chain 'B' and (resid 14 through 623 or resid 633 through 1307)) selection = (chain 'C' and (resid 14 through 623 or resid 633 through 1307)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'S' selection = chain 'Y' selection = chain 'e' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.350 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: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.800 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 : 0.005 0.075 34364 Z= 0.226 Angle : 0.708 10.868 46942 Z= 0.350 Chirality : 0.048 0.481 5502 Planarity : 0.005 0.121 5902 Dihedral : 13.651 89.727 11855 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.87 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.13), residues: 4106 helix: 1.94 (0.21), residues: 604 sheet: -0.60 (0.16), residues: 1068 loop : -1.96 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 357 TYR 0.024 0.001 TYR A 904 PHE 0.034 0.002 PHE C 329 TRP 0.073 0.002 TRP C 104 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (34227) covalent geometry : angle 0.69045 / 0.35 (46584) SS BOND : bond 0.00369 / 0.25 ( 53) SS BOND : angle 1.45666 / 0.90 ( 106) hydrogen bonds : bond 0.14936 / 9.97 ( 1006) hydrogen bonds : angle 6.64883 / 4.57 ( 2778) link_ALPHA1-3 : bond 0.00290 / 0.15 ( 3) link_ALPHA1-3 : angle 1.74638 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00406 / 0.20 ( 3) link_ALPHA1-6 : angle 1.61003 / 1.04 ( 9) link_BETA1-4 : bond 0.00446 / 0.24 ( 29) link_BETA1-4 : angle 1.71580 / 1.16 ( 87) link_NAG-ASN : bond 0.00265 / 0.16 ( 49) link_NAG-ASN : angle 2.27657 / 1.49 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 103 LYS cc_start: 0.6038 (tttp) cc_final: 0.5666 (tmtt) REVERT: E 107 LYS cc_start: 0.6934 (tptp) cc_final: 0.6586 (mmmm) REVERT: A 456 PHE cc_start: 0.7881 (m-80) cc_final: 0.7432 (m-80) REVERT: A 1002 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 517 LEU cc_start: 0.9282 (tp) cc_final: 0.8767 (tp) REVERT: C 79 PHE cc_start: 0.7528 (t80) cc_final: 0.7294 (t80) REVERT: C 495 TYR cc_start: 0.5639 (m-10) cc_final: 0.5281 (m-10) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2225 time to fit residues: 67.8626 Evaluate side-chains 120 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 43 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN C1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.107302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.066903 restraints weight = 154639.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.069145 restraints weight = 74063.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068763 restraints weight = 42724.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068768 restraints weight = 34953.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068787 restraints weight = 38222.594| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34364 Z= 0.170 Angle : 0.626 9.228 46942 Z= 0.315 Chirality : 0.044 0.242 5502 Planarity : 0.005 0.125 5902 Dihedral : 4.532 28.807 4460 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.72 % Favored : 93.01 % Rotamer: Outliers : 0.30 % Allowed : 6.00 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4106 helix: 2.03 (0.21), residues: 634 sheet: -0.57 (0.16), residues: 1041 loop : -1.92 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.023 0.001 TYR D 90 PHE 0.019 0.001 PHE B 906 TRP 0.040 0.002 TRP C 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (34227) covalent geometry : angle 0.61318 / 0.31 (46584) SS BOND : bond 0.00317 / 0.21 ( 53) SS BOND : angle 1.15700 / 0.71 ( 106) hydrogen bonds : bond 0.05168 / 3.39 ( 1006) hydrogen bonds : angle 5.43885 / 3.74 ( 2778) link_ALPHA1-3 : bond 0.00677 / 0.34 ( 3) link_ALPHA1-3 : angle 1.65469 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00400 / 0.20 ( 3) link_ALPHA1-6 : angle 1.58275 / 1.01 ( 9) link_BETA1-4 : bond 0.00416 / 0.22 ( 29) link_BETA1-4 : angle 1.66382 / 1.21 ( 87) link_NAG-ASN : bond 0.00235 / 0.13 ( 49) link_NAG-ASN : angle 1.70766 / 1.16 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4328 (ttp-170) cc_final: 0.3813 (tmt170) REVERT: H 73 MET cc_start: 0.6280 (pmm) cc_final: 0.5656 (mmp) REVERT: A 449 TYR cc_start: 0.8682 (m-80) cc_final: 0.8409 (m-80) REVERT: A 456 PHE cc_start: 0.7630 (m-80) cc_final: 0.7352 (m-80) REVERT: A 1002 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 177 MET cc_start: 0.6239 (mtt) cc_final: 0.5166 (ptp) outliers start: 11 outliers final: 10 residues processed: 140 average time/residue: 0.2049 time to fit residues: 48.1883 Evaluate side-chains 128 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 148 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 71 optimal weight: 40.0000 chunk 382 optimal weight: 7.9990 chunk 77 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 325 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 130 optimal weight: 40.0000 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.107215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066225 restraints weight = 154954.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065587 restraints weight = 70937.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.066405 restraints weight = 43305.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066852 restraints weight = 32319.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066706 restraints weight = 27590.331| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34364 Z= 0.153 Angle : 0.584 9.265 46942 Z= 0.294 Chirality : 0.043 0.244 5502 Planarity : 0.004 0.122 5902 Dihedral : 4.365 27.444 4460 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.28 % Favored : 93.45 % Rotamer: Outliers : 0.72 % Allowed : 9.34 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4106 helix: 2.35 (0.21), residues: 621 sheet: -0.49 (0.16), residues: 1034 loop : -1.89 (0.11), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.027 0.001 TYR A 904 PHE 0.014 0.001 PHE B 906 TRP 0.028 0.001 TRP C 104 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (34227) covalent geometry : angle 0.57357 / 0.29 (46584) SS BOND : bond 0.00281 / 0.19 ( 53) SS BOND : angle 0.97884 / 0.58 ( 106) hydrogen bonds : bond 0.04832 / 3.17 ( 1006) hydrogen bonds : angle 5.14538 / 3.54 ( 2778) link_ALPHA1-3 : bond 0.00715 / 0.36 ( 3) link_ALPHA1-3 : angle 1.42853 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00538 / 0.27 ( 3) link_ALPHA1-6 : angle 1.50694 / 0.97 ( 9) link_BETA1-4 : bond 0.00490 / 0.25 ( 29) link_BETA1-4 : angle 1.48013 / 1.04 ( 87) link_NAG-ASN : bond 0.00246 / 0.14 ( 49) link_NAG-ASN : angle 1.60872 / 1.10 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 MET cc_start: 0.5925 (pmm) cc_final: 0.5415 (mmp) REVERT: D 2 MET cc_start: 0.4787 (tmm) cc_final: 0.4146 (tmm) REVERT: D 90 TYR cc_start: 0.9339 (m-80) cc_final: 0.9051 (m-80) REVERT: A 1002 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8109 (tm-30) REVERT: C 489 TYR cc_start: 0.6304 (m-80) cc_final: 0.6045 (m-80) REVERT: C 1031 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7206 (mp0) outliers start: 26 outliers final: 12 residues processed: 144 average time/residue: 0.2219 time to fit residues: 53.0460 Evaluate side-chains 136 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 198 optimal weight: 6.9990 chunk 296 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 96 optimal weight: 4.9990 chunk 380 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 384 optimal weight: 3.9990 chunk 309 optimal weight: 8.9990 chunk 328 optimal weight: 0.0060 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 901 GLN C 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.107796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.067390 restraints weight = 154649.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069556 restraints weight = 71492.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.068799 restraints weight = 51709.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.069365 restraints weight = 39131.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.069412 restraints weight = 35118.570| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 34364 Z= 0.114 Angle : 0.556 9.438 46942 Z= 0.278 Chirality : 0.043 0.249 5502 Planarity : 0.004 0.117 5902 Dihedral : 4.196 27.094 4460 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.14 % Favored : 93.62 % Rotamer: Outliers : 0.94 % Allowed : 10.94 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4106 helix: 2.53 (0.21), residues: 622 sheet: -0.42 (0.16), residues: 1041 loop : -1.83 (0.12), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.031 0.001 TYR A 904 PHE 0.020 0.001 PHE C 855 TRP 0.020 0.001 TRP C 104 HIS 0.002 0.000 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (34227) covalent geometry : angle 0.54595 / 0.28 (46584) SS BOND : bond 0.00241 / 0.16 ( 53) SS BOND : angle 0.84283 / 0.50 ( 106) hydrogen bonds : bond 0.04316 / 2.83 ( 1006) hydrogen bonds : angle 4.90298 / 3.37 ( 2778) link_ALPHA1-3 : bond 0.00693 / 0.35 ( 3) link_ALPHA1-3 : angle 1.42073 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00526 / 0.26 ( 3) link_ALPHA1-6 : angle 1.46108 / 0.94 ( 9) link_BETA1-4 : bond 0.00450 / 0.24 ( 29) link_BETA1-4 : angle 1.42251 / 1.00 ( 87) link_NAG-ASN : bond 0.00164 / 0.10 ( 49) link_NAG-ASN : angle 1.47432 / 1.02 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4147 (ttp-170) cc_final: 0.3870 (tmt170) REVERT: H 73 MET cc_start: 0.6237 (pmm) cc_final: 0.5372 (mmt) REVERT: D 2 MET cc_start: 0.3958 (tmm) cc_final: 0.3115 (tmm) REVERT: D 90 TYR cc_start: 0.9438 (m-80) cc_final: 0.9177 (m-80) REVERT: E 173 TYR cc_start: 0.4719 (m-80) cc_final: 0.4464 (m-80) REVERT: A 581 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (p) REVERT: A 1002 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 177 MET cc_start: 0.5954 (mtt) cc_final: 0.5254 (ptp) REVERT: C 489 TYR cc_start: 0.6275 (m-80) cc_final: 0.6070 (m-80) outliers start: 34 outliers final: 17 residues processed: 152 average time/residue: 0.2139 time to fit residues: 54.6684 Evaluate side-chains 139 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 321 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 57 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 342 optimal weight: 4.9990 chunk 385 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.106479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064764 restraints weight = 154994.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063678 restraints weight = 70702.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064239 restraints weight = 43651.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.064703 restraints weight = 33340.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.064964 restraints weight = 28546.018| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34364 Z= 0.209 Angle : 0.610 9.324 46942 Z= 0.304 Chirality : 0.044 0.243 5502 Planarity : 0.004 0.121 5902 Dihedral : 4.311 25.808 4460 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.84 % Favored : 92.91 % Rotamer: Outliers : 1.05 % Allowed : 12.49 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4106 helix: 2.35 (0.21), residues: 629 sheet: -0.45 (0.16), residues: 1047 loop : -1.83 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.023 0.001 TYR C 904 PHE 0.021 0.001 PHE E 116 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (34227) covalent geometry : angle 0.59845 / 0.30 (46584) SS BOND : bond 0.00401 / 0.26 ( 53) SS BOND : angle 1.15830 / 0.70 ( 106) hydrogen bonds : bond 0.04947 / 3.24 ( 1006) hydrogen bonds : angle 5.03314 / 3.47 ( 2778) link_ALPHA1-3 : bond 0.00607 / 0.30 ( 3) link_ALPHA1-3 : angle 1.44888 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00453 / 0.23 ( 3) link_ALPHA1-6 : angle 1.55055 / 1.00 ( 9) link_BETA1-4 : bond 0.00409 / 0.21 ( 29) link_BETA1-4 : angle 1.42452 / 1.01 ( 87) link_NAG-ASN : bond 0.00317 / 0.20 ( 49) link_NAG-ASN : angle 1.65859 / 1.16 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 2 MET cc_start: 0.4973 (tmm) cc_final: 0.4350 (tmm) REVERT: D 90 TYR cc_start: 0.9428 (m-80) cc_final: 0.9163 (m-80) REVERT: A 581 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 1002 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 392 PHE cc_start: 0.8961 (m-80) cc_final: 0.8718 (m-80) REVERT: C 489 TYR cc_start: 0.6197 (m-80) cc_final: 0.5948 (m-80) REVERT: C 1031 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7322 (mp0) outliers start: 38 outliers final: 23 residues processed: 150 average time/residue: 0.2065 time to fit residues: 51.5276 Evaluate side-chains 139 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 345 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 179 optimal weight: 0.2980 chunk 266 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 chunk 408 optimal weight: 4.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN D 197 ASN E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 804 GLN C 370 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.106068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.064415 restraints weight = 154280.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063342 restraints weight = 70626.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063990 restraints weight = 43536.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.064628 restraints weight = 34144.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065006 restraints weight = 28232.801| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 34364 Z= 0.231 Angle : 0.624 9.301 46942 Z= 0.313 Chirality : 0.044 0.240 5502 Planarity : 0.004 0.124 5902 Dihedral : 4.409 27.074 4460 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.09 % Favored : 92.69 % Rotamer: Outliers : 1.30 % Allowed : 13.59 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4106 helix: 2.16 (0.21), residues: 637 sheet: -0.50 (0.16), residues: 1061 loop : -1.85 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 45 TYR 0.033 0.001 TYR A 904 PHE 0.022 0.002 PHE A 238 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (34227) covalent geometry : angle 0.61263 / 0.31 (46584) SS BOND : bond 0.00355 / 0.25 ( 53) SS BOND : angle 1.19019 / 0.71 ( 106) hydrogen bonds : bond 0.05141 / 3.36 ( 1006) hydrogen bonds : angle 5.10151 / 3.52 ( 2778) link_ALPHA1-3 : bond 0.00603 / 0.30 ( 3) link_ALPHA1-3 : angle 1.47954 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00480 / 0.24 ( 3) link_ALPHA1-6 : angle 1.57106 / 1.01 ( 9) link_BETA1-4 : bond 0.00423 / 0.22 ( 29) link_BETA1-4 : angle 1.43636 / 1.01 ( 87) link_NAG-ASN : bond 0.00327 / 0.21 ( 49) link_NAG-ASN : angle 1.70085 / 1.18 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4124 (tmm) REVERT: D 90 TYR cc_start: 0.9435 (m-80) cc_final: 0.9149 (m-80) REVERT: A 581 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8802 (p) REVERT: A 1002 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 392 PHE cc_start: 0.9112 (m-80) cc_final: 0.8830 (m-80) REVERT: C 177 MET cc_start: 0.4368 (mtt) cc_final: 0.3613 (ptp) REVERT: C 489 TYR cc_start: 0.6186 (m-80) cc_final: 0.5938 (m-80) REVERT: C 1031 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7312 (mp0) outliers start: 47 outliers final: 32 residues processed: 148 average time/residue: 0.2133 time to fit residues: 52.9911 Evaluate side-chains 146 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 266 optimal weight: 0.6980 chunk 315 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 163 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 277 optimal weight: 0.0970 chunk 201 optimal weight: 8.9990 chunk 387 optimal weight: 0.0370 chunk 210 optimal weight: 0.0570 chunk 232 optimal weight: 6.9990 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS C 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.108197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069503 restraints weight = 155264.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069947 restraints weight = 78131.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070353 restraints weight = 51880.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070550 restraints weight = 38192.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.070682 restraints weight = 34471.401| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 34364 Z= 0.100 Angle : 0.559 9.435 46942 Z= 0.279 Chirality : 0.043 0.256 5502 Planarity : 0.004 0.113 5902 Dihedral : 4.095 29.763 4460 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.67 % Favored : 94.11 % Rotamer: Outliers : 1.13 % Allowed : 13.87 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4106 helix: 2.72 (0.21), residues: 615 sheet: -0.33 (0.16), residues: 1054 loop : -1.75 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 45 TYR 0.017 0.001 TYR H 90 PHE 0.020 0.001 PHE E 116 TRP 0.017 0.001 TRP C 104 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (34227) covalent geometry : angle 0.54950 / 0.28 (46584) SS BOND : bond 0.00221 / 0.14 ( 53) SS BOND : angle 0.89430 / 0.56 ( 106) hydrogen bonds : bond 0.03950 / 2.59 ( 1006) hydrogen bonds : angle 4.68630 / 3.24 ( 2778) link_ALPHA1-3 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-3 : angle 1.45529 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00584 / 0.29 ( 3) link_ALPHA1-6 : angle 1.41242 / 0.92 ( 9) link_BETA1-4 : bond 0.00500 / 0.28 ( 29) link_BETA1-4 : angle 1.37963 / 0.96 ( 87) link_NAG-ASN : bond 0.00266 / 0.17 ( 49) link_NAG-ASN : angle 1.44792 / 1.00 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 MET cc_start: 0.6409 (pmm) cc_final: 0.5406 (mmm) REVERT: D 2 MET cc_start: 0.3276 (OUTLIER) cc_final: 0.2432 (tmm) REVERT: D 90 TYR cc_start: 0.9454 (m-80) cc_final: 0.9223 (m-80) REVERT: A 581 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8823 (p) REVERT: B 392 PHE cc_start: 0.9083 (m-80) cc_final: 0.8853 (m-80) REVERT: C 104 TRP cc_start: 0.8449 (m-90) cc_final: 0.8198 (m-10) REVERT: C 489 TYR cc_start: 0.6330 (m-80) cc_final: 0.6096 (m-80) REVERT: C 1031 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7406 (mp0) outliers start: 41 outliers final: 21 residues processed: 163 average time/residue: 0.2064 time to fit residues: 56.8113 Evaluate side-chains 145 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 175 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 30.0000 chunk 394 optimal weight: 0.9990 chunk 234 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.106000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064941 restraints weight = 154324.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066482 restraints weight = 72284.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.065667 restraints weight = 49230.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066545 restraints weight = 39016.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066509 restraints weight = 31075.859| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 34364 Z= 0.238 Angle : 0.635 9.350 46942 Z= 0.316 Chirality : 0.044 0.275 5502 Planarity : 0.004 0.119 5902 Dihedral : 4.325 28.523 4460 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.77 % Favored : 92.99 % Rotamer: Outliers : 0.99 % Allowed : 14.15 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4106 helix: 2.36 (0.21), residues: 630 sheet: -0.45 (0.16), residues: 1059 loop : -1.80 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 45 TYR 0.032 0.001 TYR A 904 PHE 0.023 0.001 PHE A 238 TRP 0.017 0.001 TRP C 104 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (34227) covalent geometry : angle 0.62300 / 0.31 (46584) SS BOND : bond 0.00351 / 0.24 ( 53) SS BOND : angle 1.35823 / 0.80 ( 106) hydrogen bonds : bond 0.05037 / 3.29 ( 1006) hydrogen bonds : angle 4.95491 / 3.42 ( 2778) link_ALPHA1-3 : bond 0.00571 / 0.28 ( 3) link_ALPHA1-3 : angle 1.48822 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00444 / 0.22 ( 3) link_ALPHA1-6 : angle 1.58764 / 1.02 ( 9) link_BETA1-4 : bond 0.00403 / 0.21 ( 29) link_BETA1-4 : angle 1.42648 / 1.01 ( 87) link_NAG-ASN : bond 0.00363 / 0.23 ( 49) link_NAG-ASN : angle 1.68972 / 1.18 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.344 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: D 2 MET cc_start: 0.4044 (OUTLIER) cc_final: 0.3223 (tmm) REVERT: D 90 TYR cc_start: 0.9507 (m-80) cc_final: 0.9294 (m-80) REVERT: A 581 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8751 (p) REVERT: C 63 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7236 (m) REVERT: C 104 TRP cc_start: 0.8511 (m-90) cc_final: 0.8228 (m-10) REVERT: C 177 MET cc_start: 0.5690 (mtt) cc_final: 0.4763 (ptp) REVERT: C 489 TYR cc_start: 0.6201 (m-80) cc_final: 0.5977 (m-80) REVERT: C 1031 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7396 (mp0) outliers start: 36 outliers final: 28 residues processed: 146 average time/residue: 0.2033 time to fit residues: 49.7949 Evaluate side-chains 146 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 218 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 chunk 9 optimal weight: 50.0000 chunk 258 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064564 restraints weight = 154561.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.063401 restraints weight = 70238.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.063862 restraints weight = 43343.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.064341 restraints weight = 33514.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064719 restraints weight = 28333.948| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 34364 Z= 0.198 Angle : 0.610 9.455 46942 Z= 0.304 Chirality : 0.044 0.268 5502 Planarity : 0.004 0.119 5902 Dihedral : 4.350 28.039 4460 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.43 % Favored : 93.33 % Rotamer: Outliers : 1.16 % Allowed : 14.20 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4106 helix: 2.33 (0.21), residues: 631 sheet: -0.47 (0.16), residues: 1058 loop : -1.82 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.031 0.001 TYR D 100C PHE 0.021 0.001 PHE A 238 TRP 0.019 0.001 TRP C 104 HIS 0.003 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (34227) covalent geometry : angle 0.59839 / 0.30 (46584) SS BOND : bond 0.00328 / 0.23 ( 53) SS BOND : angle 1.22657 / 0.71 ( 106) hydrogen bonds : bond 0.04888 / 3.19 ( 1006) hydrogen bonds : angle 4.91238 / 3.38 ( 2778) link_ALPHA1-3 : bond 0.00569 / 0.28 ( 3) link_ALPHA1-3 : angle 1.48760 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00497 / 0.25 ( 3) link_ALPHA1-6 : angle 1.54055 / 1.00 ( 9) link_BETA1-4 : bond 0.00410 / 0.21 ( 29) link_BETA1-4 : angle 1.39733 / 0.98 ( 87) link_NAG-ASN : bond 0.00265 / 0.17 ( 49) link_NAG-ASN : angle 1.65571 / 1.16 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 MET cc_start: 0.5726 (pmm) cc_final: 0.5024 (mmm) REVERT: D 2 MET cc_start: 0.5157 (OUTLIER) cc_final: 0.4643 (tmm) REVERT: A 581 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8769 (p) REVERT: C 63 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7499 (m) REVERT: C 104 TRP cc_start: 0.8720 (m-90) cc_final: 0.8312 (m-10) REVERT: C 177 MET cc_start: 0.4472 (mtt) cc_final: 0.3646 (ptp) REVERT: C 489 TYR cc_start: 0.6125 (m-80) cc_final: 0.5903 (m-80) REVERT: C 1031 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7407 (mp0) outliers start: 42 outliers final: 33 residues processed: 149 average time/residue: 0.1965 time to fit residues: 49.5933 Evaluate side-chains 149 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 13 optimal weight: 7.9990 chunk 392 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 240 optimal weight: 30.0000 chunk 326 optimal weight: 5.9990 chunk 378 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 405 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 105 GLN D 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.102238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058850 restraints weight = 131976.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060525 restraints weight = 58660.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061554 restraints weight = 37425.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.062109 restraints weight = 28857.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062505 restraints weight = 25097.667| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 34364 Z= 0.192 Angle : 0.615 12.375 46942 Z= 0.305 Chirality : 0.044 0.245 5502 Planarity : 0.004 0.120 5902 Dihedral : 4.370 32.070 4460 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.72 % Favored : 93.03 % Rotamer: Outliers : 1.05 % Allowed : 14.51 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4106 helix: 2.34 (0.21), residues: 630 sheet: -0.46 (0.16), residues: 1047 loop : -1.83 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 142 TYR 0.034 0.001 TYR D 100C PHE 0.020 0.001 PHE A 238 TRP 0.020 0.001 TRP C 104 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (34227) covalent geometry : angle 0.60358 / 0.30 (46584) SS BOND : bond 0.00329 / 0.22 ( 53) SS BOND : angle 1.17399 / 0.68 ( 106) hydrogen bonds : bond 0.04854 / 3.17 ( 1006) hydrogen bonds : angle 4.89540 / 3.37 ( 2778) link_ALPHA1-3 : bond 0.00558 / 0.28 ( 3) link_ALPHA1-3 : angle 1.48909 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00496 / 0.25 ( 3) link_ALPHA1-6 : angle 1.53811 / 1.00 ( 9) link_BETA1-4 : bond 0.00397 / 0.20 ( 29) link_BETA1-4 : angle 1.40373 / 0.99 ( 87) link_NAG-ASN : bond 0.00270 / 0.17 ( 49) link_NAG-ASN : angle 1.66380 / 1.16 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8212 Ramachandran restraints generated. 4106 Oldfield, 0 Emsley, 4106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 ILE cc_start: 0.3393 (OUTLIER) cc_final: 0.3166 (tt) REVERT: H 73 MET cc_start: 0.6811 (pmm) cc_final: 0.5411 (mmm) REVERT: D 2 MET cc_start: 0.2095 (OUTLIER) cc_final: 0.1278 (tmm) REVERT: A 581 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8771 (p) REVERT: C 63 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7483 (m) REVERT: C 104 TRP cc_start: 0.8713 (m-90) cc_final: 0.8288 (m-10) REVERT: C 489 TYR cc_start: 0.6336 (m-80) cc_final: 0.6130 (m-80) REVERT: C 1031 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7376 (mp0) outliers start: 38 outliers final: 29 residues processed: 140 average time/residue: 0.2077 time to fit residues: 48.6156 Evaluate side-chains 145 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1148 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 27 optimal weight: 0.4980 chunk 24 optimal weight: 30.0000 chunk 305 optimal weight: 2.9990 chunk 80 optimal weight: 40.0000 chunk 78 optimal weight: 5.9990 chunk 408 optimal weight: 1.9990 chunk 402 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 276 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.102442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059683 restraints weight = 131425.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061385 restraints weight = 56899.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062445 restraints weight = 35670.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063091 restraints weight = 27213.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063460 restraints weight = 23258.008| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34364 Z= 0.111 Angle : 0.568 10.143 46942 Z= 0.283 Chirality : 0.043 0.253 5502 Planarity : 0.004 0.114 5902 Dihedral : 4.193 30.308 4460 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.92 % Favored : 93.84 % Rotamer: Outliers : 1.05 % Allowed : 14.48 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4106 helix: 2.62 (0.22), residues: 616 sheet: -0.37 (0.16), residues: 1071 loop : -1.76 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.032 0.001 TYR D 100C PHE 0.019 0.001 PHE E 116 TRP 0.018 0.001 TRP C 104 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (34227) covalent geometry : angle 0.55779 / 0.28 (46584) SS BOND : bond 0.00243 / 0.16 ( 53) SS BOND : angle 1.00475 / 0.58 ( 106) hydrogen bonds : bond 0.04239 / 2.78 ( 1006) hydrogen bonds : angle 4.68801 / 3.23 ( 2778) link_ALPHA1-3 : bond 0.00580 / 0.29 ( 3) link_ALPHA1-3 : angle 1.47948 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00542 / 0.27 ( 3) link_ALPHA1-6 : angle 1.45513 / 0.95 ( 9) link_BETA1-4 : bond 0.00433 / 0.23 ( 29) link_BETA1-4 : angle 1.36805 / 0.96 ( 87) link_NAG-ASN : bond 0.00174 / 0.11 ( 49) link_NAG-ASN : angle 1.51306 / 1.05 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8637.76 seconds wall clock time: 148 minutes 49.10 seconds (8929.10 seconds total)