Starting phenix.real_space_refine on Wed Apr 8 02:48:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrt_23499/04_2026/7lrt_23499.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrt_23499/04_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_23499/04_2026/7lrt_23499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrt_23499/04_2026/7lrt_23499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lrt_23499/04_2026/7lrt_23499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrt_23499/04_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): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 15 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 dihedrals: 30 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 dihedrals: 21 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.61, per 1000 atoms: 0.23 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 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: 1.34 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: 8.46 Time building geometry restraints manager: 3.80 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 - 22.87: 19993 22.87 - 45.73: 1203 45.73 - 68.60: 178 68.60 - 91.47: 83 91.47 - 114.34: 45 Dihedral angle restraints: 21502 sinusoidal: 9442 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 21499 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: 12.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.570 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 15.670 114.337 13593 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 covalent geometry : bond 0.00504 (34227) covalent geometry : angle 0.69045 (46584) SS BOND : bond 0.00369 ( 53) SS BOND : angle 1.45666 ( 106) hydrogen bonds : bond 0.14936 ( 1006) hydrogen bonds : angle 6.64883 ( 2778) link_ALPHA1-3 : bond 0.00290 ( 3) link_ALPHA1-3 : angle 1.74638 ( 9) link_ALPHA1-6 : bond 0.00406 ( 3) link_ALPHA1-6 : angle 1.61003 ( 9) link_BETA1-4 : bond 0.00446 ( 29) link_BETA1-4 : angle 1.71580 ( 87) link_NAG-ASN : bond 0.00265 ( 49) link_NAG-ASN : angle 2.27657 ( 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 : 1.153 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: 0.2131 time to fit residues: 64.3793 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 : 1.121 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066687 restraints weight = 154651.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.068212 restraints weight = 71889.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067751 restraints weight = 49110.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068366 restraints weight = 39123.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068515 restraints weight = 32128.015| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34364 Z= 0.169 Angle : 0.636 9.997 46942 Z= 0.317 Chirality : 0.045 0.264 5502 Planarity : 0.005 0.125 5902 Dihedral : 11.095 102.308 6198 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.65 % Favored : 93.08 % Rotamer: Outliers : 0.28 % Allowed : 5.72 % Favored : 94.00 % 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: -1.33 (0.13), residues: 4106 helix: 2.00 (0.21), residues: 636 sheet: -0.56 (0.16), residues: 1040 loop : -1.92 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.022 0.001 TYR A 904 PHE 0.018 0.001 PHE B 906 TRP 0.038 0.001 TRP C 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00389 (34227) covalent geometry : angle 0.62178 (46584) SS BOND : bond 0.00317 ( 53) SS BOND : angle 1.14433 ( 106) hydrogen bonds : bond 0.05338 ( 1006) hydrogen bonds : angle 5.51499 ( 2778) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 2.34894 ( 9) link_ALPHA1-6 : bond 0.00849 ( 3) link_ALPHA1-6 : angle 1.41165 ( 9) link_BETA1-4 : bond 0.00516 ( 29) link_BETA1-4 : angle 1.95629 ( 87) link_NAG-ASN : bond 0.00221 ( 49) link_NAG-ASN : angle 1.78108 ( 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 141 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4294 (ttp-170) cc_final: 0.3837 (tmt170) REVERT: A 456 PHE cc_start: 0.7598 (m-80) cc_final: 0.7327 (m-80) REVERT: A 1002 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8168 (tm-30) outliers start: 10 outliers final: 9 residues processed: 136 average time/residue: 0.1930 time to fit residues: 44.0370 Evaluate side-chains 127 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 256 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 71 optimal weight: 50.0000 chunk 382 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 283 optimal weight: 0.7980 chunk 325 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 197 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 271 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 = 0.4109 r_free = 0.4109 target = 0.106065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064614 restraints weight = 154910.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063991 restraints weight = 71108.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064768 restraints weight = 43638.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 80)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064092 restraints weight = 33522.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.064207 restraints weight = 29072.806| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 34364 Z= 0.245 Angle : 0.661 9.298 46942 Z= 0.329 Chirality : 0.045 0.232 5502 Planarity : 0.005 0.129 5902 Dihedral : 9.276 96.342 6198 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.18 % Favored : 92.55 % Rotamer: Outliers : 0.94 % Allowed : 9.62 % Favored : 89.44 % 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: -1.37 (0.13), residues: 4106 helix: 1.91 (0.21), residues: 644 sheet: -0.63 (0.16), residues: 1066 loop : -1.93 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.027 0.002 TYR A 904 PHE 0.023 0.002 PHE B 906 TRP 0.035 0.002 TRP C 104 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00569 (34227) covalent geometry : angle 0.64711 (46584) SS BOND : bond 0.00379 ( 53) SS BOND : angle 1.13770 ( 106) hydrogen bonds : bond 0.05476 ( 1006) hydrogen bonds : angle 5.40137 ( 2778) link_ALPHA1-3 : bond 0.01082 ( 3) link_ALPHA1-3 : angle 1.57078 ( 9) link_ALPHA1-6 : bond 0.00962 ( 3) link_ALPHA1-6 : angle 1.41244 ( 9) link_BETA1-4 : bond 0.00428 ( 29) link_BETA1-4 : angle 1.90877 ( 87) link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 1.86389 ( 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 159 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 MET cc_start: 0.5761 (pmm) cc_final: 0.5285 (mmp) REVERT: D 2 MET cc_start: 0.4828 (tmm) cc_final: 0.4187 (tmm) REVERT: D 90 TYR cc_start: 0.9300 (m-80) cc_final: 0.9025 (m-80) REVERT: D 100 TYR cc_start: 0.7005 (t80) cc_final: 0.6776 (t80) REVERT: A 740 MET cc_start: 0.9066 (ttt) cc_final: 0.8842 (ttp) REVERT: A 1002 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 177 MET cc_start: 0.4449 (mtt) cc_final: 0.3721 (ptp) REVERT: C 489 TYR cc_start: 0.6297 (m-80) cc_final: 0.6072 (m-80) REVERT: C 1031 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7205 (mp0) outliers start: 34 outliers final: 16 residues processed: 151 average time/residue: 0.1749 time to fit residues: 45.2143 Evaluate side-chains 134 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 914 ASN 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: 4.9990 chunk 296 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 380 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 267 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 384 optimal weight: 0.7980 chunk 309 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4138 r_free = 0.4138 target = 0.107600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066914 restraints weight = 154425.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.066469 restraints weight = 69620.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066607 restraints weight = 42852.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066799 restraints weight = 32407.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.067034 restraints weight = 27736.401| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 34364 Z= 0.117 Angle : 0.572 9.495 46942 Z= 0.285 Chirality : 0.044 0.236 5502 Planarity : 0.004 0.121 5902 Dihedral : 7.996 91.228 6198 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.72 % Rotamer: Outliers : 0.80 % Allowed : 11.30 % Favored : 87.90 % 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: -1.12 (0.13), residues: 4106 helix: 2.48 (0.21), residues: 622 sheet: -0.44 (0.16), residues: 1036 loop : -1.86 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.032 0.001 TYR A 904 PHE 0.012 0.001 PHE A 927 TRP 0.022 0.001 TRP C 104 HIS 0.002 0.000 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00262 (34227) covalent geometry : angle 0.55931 (46584) SS BOND : bond 0.00253 ( 53) SS BOND : angle 0.89530 ( 106) hydrogen bonds : bond 0.04469 ( 1006) hydrogen bonds : angle 4.97407 ( 2778) link_ALPHA1-3 : bond 0.01073 ( 3) link_ALPHA1-3 : angle 1.62090 ( 9) link_ALPHA1-6 : bond 0.01111 ( 3) link_ALPHA1-6 : angle 1.46179 ( 9) link_BETA1-4 : bond 0.00490 ( 29) link_BETA1-4 : angle 1.74581 ( 87) link_NAG-ASN : bond 0.00192 ( 49) link_NAG-ASN : angle 1.58221 ( 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 158 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 MET cc_start: 0.5907 (pmm) cc_final: 0.5204 (mmt) REVERT: D 2 MET cc_start: 0.4633 (tmm) cc_final: 0.3850 (tmm) REVERT: D 90 TYR cc_start: 0.9393 (m-80) cc_final: 0.9120 (m-80) REVERT: A 1002 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7998 (tm-30) REVERT: B 902 MET cc_start: 0.9440 (tpt) cc_final: 0.9193 (tpt) REVERT: C 177 MET cc_start: 0.4415 (mtt) cc_final: 0.3565 (ptp) REVERT: C 489 TYR cc_start: 0.6254 (m-80) cc_final: 0.6003 (m-80) outliers start: 29 outliers final: 14 residues processed: 150 average time/residue: 0.1923 time to fit residues: 48.4414 Evaluate side-chains 135 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain A residue 620 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 197 ILE Chi-restraints excluded: chain B residue 400 PHE 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: 3.9990 chunk 303 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 136 optimal weight: 0.1980 chunk 342 optimal weight: 4.9990 chunk 385 optimal weight: 0.6980 chunk 72 optimal weight: 50.0000 chunk 271 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN D 197 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.106878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.066587 restraints weight = 154870.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068143 restraints weight = 73619.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.067751 restraints weight = 47329.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.068163 restraints weight = 39583.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068428 restraints weight = 33236.877| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34364 Z= 0.164 Angle : 0.588 9.405 46942 Z= 0.293 Chirality : 0.043 0.236 5502 Planarity : 0.004 0.121 5902 Dihedral : 7.557 89.778 6198 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.43 % Favored : 93.33 % Rotamer: Outliers : 0.97 % Allowed : 12.79 % Favored : 86.24 % 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: 2.48 (0.21), residues: 624 sheet: -0.45 (0.16), residues: 1046 loop : -1.81 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.020 0.001 TYR C 904 PHE 0.020 0.001 PHE C 855 TRP 0.018 0.001 TRP C 104 HIS 0.002 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00381 (34227) covalent geometry : angle 0.57557 (46584) SS BOND : bond 0.00281 ( 53) SS BOND : angle 1.11160 ( 106) hydrogen bonds : bond 0.04686 ( 1006) hydrogen bonds : angle 4.96148 ( 2778) link_ALPHA1-3 : bond 0.00964 ( 3) link_ALPHA1-3 : angle 1.55635 ( 9) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.59112 ( 9) link_BETA1-4 : bond 0.00402 ( 29) link_BETA1-4 : angle 1.62475 ( 87) link_NAG-ASN : bond 0.00233 ( 49) link_NAG-ASN : angle 1.65452 ( 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 156 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4338 (ttp-170) cc_final: 0.3936 (tmt170) REVERT: H 73 MET cc_start: 0.6338 (pmm) cc_final: 0.5355 (mmt) REVERT: D 2 MET cc_start: 0.3275 (tmm) cc_final: 0.2415 (tmm) REVERT: D 90 TYR cc_start: 0.9454 (m-80) cc_final: 0.9184 (m-80) REVERT: A 1002 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 902 MET cc_start: 0.9520 (tpt) cc_final: 0.9218 (tpt) REVERT: C 177 MET cc_start: 0.5812 (mtt) cc_final: 0.4835 (ptp) REVERT: C 489 TYR cc_start: 0.6345 (m-80) cc_final: 0.6095 (m-80) REVERT: C 1031 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7284 (mp0) outliers start: 35 outliers final: 24 residues processed: 144 average time/residue: 0.1907 time to fit residues: 45.8064 Evaluate side-chains 140 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 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 171 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 345 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 312 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 67 optimal weight: 40.0000 chunk 94 optimal weight: 5.9990 chunk 179 optimal weight: 0.0770 chunk 266 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 chunk 408 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN D 39 GLN D 197 ASN E 38 GLN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 901 GLN C 185 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.105810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065175 restraints weight = 153649.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066628 restraints weight = 73081.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.066025 restraints weight = 47913.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066783 restraints weight = 38341.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066883 restraints weight = 31011.651| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34364 Z= 0.217 Angle : 0.624 9.329 46942 Z= 0.312 Chirality : 0.044 0.230 5502 Planarity : 0.004 0.124 5902 Dihedral : 7.329 88.116 6198 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.18 % Favored : 92.60 % Rotamer: Outliers : 1.44 % Allowed : 13.65 % Favored : 84.91 % 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: 2.17 (0.21), residues: 638 sheet: -0.54 (0.16), residues: 1073 loop : -1.83 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.019 0.001 TYR B1067 PHE 0.022 0.001 PHE A 238 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00505 (34227) covalent geometry : angle 0.61085 (46584) SS BOND : bond 0.00360 ( 53) SS BOND : angle 1.20186 ( 106) hydrogen bonds : bond 0.05147 ( 1006) hydrogen bonds : angle 5.08573 ( 2778) link_ALPHA1-3 : bond 0.00979 ( 3) link_ALPHA1-3 : angle 1.56966 ( 9) link_ALPHA1-6 : bond 0.01122 ( 3) link_ALPHA1-6 : angle 1.76139 ( 9) link_BETA1-4 : bond 0.00377 ( 29) link_BETA1-4 : angle 1.56036 ( 87) link_NAG-ASN : bond 0.00315 ( 49) link_NAG-ASN : angle 1.76851 ( 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 171 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4206 (ttp-170) cc_final: 0.3873 (tmt170) REVERT: D 2 MET cc_start: 0.3508 (OUTLIER) cc_final: 0.2606 (tmm) REVERT: D 66 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7277 (ppt170) REVERT: D 85 GLU cc_start: 0.7039 (tp30) cc_final: 0.6505 (pt0) REVERT: D 90 TYR cc_start: 0.9449 (m-80) cc_final: 0.9161 (m-80) REVERT: E 105 GLU cc_start: 0.2278 (OUTLIER) cc_final: 0.1893 (tt0) REVERT: A 1002 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 855 PHE cc_start: 0.7016 (m-10) cc_final: 0.6816 (m-10) REVERT: B 902 MET cc_start: 0.9491 (tpt) cc_final: 0.9265 (tpt) REVERT: C 104 TRP cc_start: 0.8573 (m-10) cc_final: 0.8149 (m-10) REVERT: C 489 TYR cc_start: 0.6272 (m-80) cc_final: 0.6035 (m-80) REVERT: C 1031 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7290 (mp0) outliers start: 52 outliers final: 31 residues processed: 156 average time/residue: 0.1822 time to fit residues: 48.0205 Evaluate side-chains 147 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 105 GLU 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 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 934 ILE 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 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: 2.9990 chunk 315 optimal weight: 0.0770 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 40.0000 chunk 163 optimal weight: 0.9990 chunk 58 optimal weight: 50.0000 chunk 277 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 387 optimal weight: 0.9990 chunk 210 optimal weight: 0.0570 chunk 232 optimal weight: 6.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS C 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.107761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067704 restraints weight = 155092.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069370 restraints weight = 70587.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.068914 restraints weight = 49002.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.069624 restraints weight = 37337.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.069583 restraints weight = 31142.229| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1990 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= 0.102 Angle : 0.558 9.494 46942 Z= 0.279 Chirality : 0.043 0.240 5502 Planarity : 0.004 0.115 5902 Dihedral : 6.847 84.749 6198 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.82 % Favored : 93.96 % Rotamer: Outliers : 1.02 % Allowed : 14.12 % 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: -0.97 (0.13), residues: 4106 helix: 2.70 (0.21), residues: 615 sheet: -0.37 (0.16), residues: 1060 loop : -1.76 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.030 0.001 TYR D 100C PHE 0.025 0.001 PHE C 855 TRP 0.018 0.001 TRP C 104 HIS 0.002 0.000 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00226 (34227) covalent geometry : angle 0.54711 (46584) SS BOND : bond 0.00236 ( 53) SS BOND : angle 0.92373 ( 106) hydrogen bonds : bond 0.04146 ( 1006) hydrogen bonds : angle 4.73767 ( 2778) link_ALPHA1-3 : bond 0.00977 ( 3) link_ALPHA1-3 : angle 1.32285 ( 9) link_ALPHA1-6 : bond 0.01110 ( 3) link_ALPHA1-6 : angle 1.81592 ( 9) link_BETA1-4 : bond 0.00455 ( 29) link_BETA1-4 : angle 1.53387 ( 87) link_NAG-ASN : bond 0.00204 ( 49) link_NAG-ASN : angle 1.54058 ( 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 160 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4079 (ttp-170) cc_final: 0.3814 (tmt170) REVERT: D 2 MET cc_start: 0.3815 (tmm) cc_final: 0.2981 (tmm) REVERT: D 66 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7324 (ppt170) REVERT: D 90 TYR cc_start: 0.9483 (m-80) cc_final: 0.9243 (m-80) REVERT: E 105 GLU cc_start: 0.2265 (OUTLIER) cc_final: 0.1388 (tt0) REVERT: B 855 PHE cc_start: 0.7041 (m-10) cc_final: 0.6838 (m-10) REVERT: C 104 TRP cc_start: 0.8443 (m-90) cc_final: 0.8174 (m-10) REVERT: C 489 TYR cc_start: 0.6297 (m-80) cc_final: 0.6074 (m-80) REVERT: C 1031 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7336 (mp0) outliers start: 37 outliers final: 22 residues processed: 150 average time/residue: 0.1943 time to fit residues: 48.1687 Evaluate side-chains 140 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 105 GLU 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 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 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 1148 PHE Chi-restraints excluded: chain C residue 132 GLU 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 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 175 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 394 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 308 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.100571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057028 restraints weight = 132474.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058669 restraints weight = 58312.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059706 restraints weight = 37167.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060315 restraints weight = 28460.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.060634 restraints weight = 24531.029| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34364 Z= 0.219 Angle : 0.619 9.346 46942 Z= 0.310 Chirality : 0.044 0.234 5502 Planarity : 0.004 0.119 5902 Dihedral : 6.974 84.161 6198 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.11 % Favored : 92.67 % Rotamer: Outliers : 1.33 % Allowed : 14.20 % Favored : 84.47 % 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: -1.10 (0.13), residues: 4106 helix: 2.38 (0.21), residues: 630 sheet: -0.45 (0.16), residues: 1059 loop : -1.81 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 45 TYR 0.030 0.001 TYR A 904 PHE 0.021 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 covalent geometry : bond 0.00511 (34227) covalent geometry : angle 0.60720 (46584) SS BOND : bond 0.00340 ( 53) SS BOND : angle 1.10990 ( 106) hydrogen bonds : bond 0.04953 ( 1006) hydrogen bonds : angle 4.94356 ( 2778) link_ALPHA1-3 : bond 0.00881 ( 3) link_ALPHA1-3 : angle 1.41228 ( 9) link_ALPHA1-6 : bond 0.01006 ( 3) link_ALPHA1-6 : angle 1.82047 ( 9) link_BETA1-4 : bond 0.00446 ( 29) link_BETA1-4 : angle 1.56488 ( 87) link_NAG-ASN : bond 0.00326 ( 49) link_NAG-ASN : angle 1.74521 ( 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 162 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.4581 (ttp-170) cc_final: 0.3914 (tmt170) REVERT: D 2 MET cc_start: 0.1926 (OUTLIER) cc_final: 0.1148 (tmm) REVERT: D 66 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7147 (ppt170) REVERT: D 90 TYR cc_start: 0.9375 (m-80) cc_final: 0.9164 (m-80) REVERT: E 48 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6303 (mm) REVERT: E 105 GLU cc_start: 0.2148 (OUTLIER) cc_final: 0.0844 (tt0) REVERT: B 855 PHE cc_start: 0.7223 (m-10) cc_final: 0.7022 (m-10) REVERT: C 63 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7485 (m) REVERT: C 104 TRP cc_start: 0.8719 (m-90) cc_final: 0.8256 (m-10) REVERT: C 489 TYR cc_start: 0.6300 (m-80) cc_final: 0.6082 (m-80) REVERT: C 1031 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7406 (mp0) outliers start: 48 outliers final: 32 residues processed: 149 average time/residue: 0.1917 time to fit residues: 47.7458 Evaluate side-chains 151 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 105 GLU 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 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 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 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 1136 THR 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: 7.9990 chunk 133 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 258 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 107 optimal weight: 0.4980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.102163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.058987 restraints weight = 132496.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060551 restraints weight = 58666.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061523 restraints weight = 37110.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062145 restraints weight = 28729.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062520 restraints weight = 24696.830| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2130 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= 0.146 Angle : 0.585 11.058 46942 Z= 0.291 Chirality : 0.043 0.235 5502 Planarity : 0.004 0.117 5902 Dihedral : 6.829 82.722 6198 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.23 % Favored : 93.52 % Rotamer: Outliers : 1.13 % Allowed : 14.56 % Favored : 84.31 % 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: -1.06 (0.13), residues: 4106 helix: 2.46 (0.21), residues: 624 sheet: -0.40 (0.16), residues: 1050 loop : -1.80 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.030 0.001 TYR D 100C PHE 0.028 0.001 PHE C 855 TRP 0.018 0.001 TRP C 104 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00339 (34227) covalent geometry : angle 0.57198 (46584) SS BOND : bond 0.00338 ( 53) SS BOND : angle 1.23064 ( 106) hydrogen bonds : bond 0.04564 ( 1006) hydrogen bonds : angle 4.79500 ( 2778) link_ALPHA1-3 : bond 0.00893 ( 3) link_ALPHA1-3 : angle 1.31360 ( 9) link_ALPHA1-6 : bond 0.01031 ( 3) link_ALPHA1-6 : angle 1.79797 ( 9) link_BETA1-4 : bond 0.00398 ( 29) link_BETA1-4 : angle 1.52885 ( 87) link_NAG-ASN : bond 0.00179 ( 49) link_NAG-ASN : angle 1.62618 ( 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 158 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 ILE cc_start: 0.3375 (OUTLIER) cc_final: 0.3108 (tt) REVERT: H 38 ARG cc_start: 0.4606 (ttp-170) cc_final: 0.3959 (tmt170) REVERT: D 2 MET cc_start: 0.1997 (OUTLIER) cc_final: 0.1227 (tmm) REVERT: D 66 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7190 (ppt170) REVERT: E 105 GLU cc_start: 0.1421 (OUTLIER) cc_final: 0.0874 (tt0) REVERT: A 449 TYR cc_start: 0.8753 (m-10) cc_final: 0.8501 (m-80) REVERT: B 855 PHE cc_start: 0.7252 (m-10) cc_final: 0.7041 (m-10) REVERT: B 902 MET cc_start: 0.9595 (tpt) cc_final: 0.9291 (tpt) REVERT: C 63 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7463 (m) REVERT: C 104 TRP cc_start: 0.8696 (m-90) cc_final: 0.8260 (m-10) REVERT: C 489 TYR cc_start: 0.6348 (m-80) cc_final: 0.6132 (m-80) REVERT: C 1031 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7388 (mp0) outliers start: 41 outliers final: 30 residues processed: 146 average time/residue: 0.2027 time to fit residues: 48.4199 Evaluate side-chains 151 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 ILE 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 66 ARG Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 105 GLU 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 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 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 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 1136 THR 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: 6.9990 chunk 392 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 326 optimal weight: 10.0000 chunk 378 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 257 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 405 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.100637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057355 restraints weight = 132266.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059020 restraints weight = 57175.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060076 restraints weight = 35896.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.060658 restraints weight = 27306.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061057 restraints weight = 23507.232| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34364 Z= 0.164 Angle : 0.592 9.378 46942 Z= 0.295 Chirality : 0.043 0.235 5502 Planarity : 0.004 0.116 5902 Dihedral : 6.810 81.540 6198 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.62 % Favored : 93.13 % Rotamer: Outliers : 1.16 % Allowed : 14.59 % Favored : 84.25 % 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: -1.05 (0.13), residues: 4106 helix: 2.45 (0.21), residues: 624 sheet: -0.38 (0.16), residues: 1038 loop : -1.80 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 45 TYR 0.031 0.001 TYR D 100C PHE 0.017 0.001 PHE A 238 TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00383 (34227) covalent geometry : angle 0.57853 (46584) SS BOND : bond 0.00325 ( 53) SS BOND : angle 1.33968 ( 106) hydrogen bonds : bond 0.04596 ( 1006) hydrogen bonds : angle 4.79734 ( 2778) link_ALPHA1-3 : bond 0.00863 ( 3) link_ALPHA1-3 : angle 1.31552 ( 9) link_ALPHA1-6 : bond 0.00996 ( 3) link_ALPHA1-6 : angle 1.76987 ( 9) link_BETA1-4 : bond 0.00391 ( 29) link_BETA1-4 : angle 1.53176 ( 87) link_NAG-ASN : bond 0.00207 ( 49) link_NAG-ASN : angle 1.65858 ( 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 158 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 ILE cc_start: 0.3349 (OUTLIER) cc_final: 0.3109 (tt) REVERT: H 38 ARG cc_start: 0.4611 (ttp-170) cc_final: 0.3955 (tmt170) REVERT: D 2 MET cc_start: 0.1986 (OUTLIER) cc_final: 0.1204 (tmm) REVERT: E 105 GLU cc_start: 0.1537 (OUTLIER) cc_final: 0.0540 (tt0) REVERT: B 855 PHE cc_start: 0.7368 (m-10) cc_final: 0.7148 (m-10) REVERT: B 902 MET cc_start: 0.9564 (tpt) cc_final: 0.9247 (tpt) REVERT: C 63 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7452 (m) REVERT: C 104 TRP cc_start: 0.8709 (m-90) cc_final: 0.8308 (m-10) REVERT: C 489 TYR cc_start: 0.6307 (m-80) cc_final: 0.6103 (m-80) REVERT: C 1031 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7402 (mp0) outliers start: 42 outliers final: 31 residues processed: 146 average time/residue: 0.1931 time to fit residues: 46.8817 Evaluate side-chains 147 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 ILE 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 105 GLU 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 742 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR 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 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 379 CYS 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 1136 THR 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: 7.9990 chunk 24 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 80 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 408 optimal weight: 2.9990 chunk 402 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 276 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4102 r_free = 0.4102 target = 0.105572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065618 restraints weight = 153538.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.067220 restraints weight = 74799.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.067019 restraints weight = 47736.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.067073 restraints weight = 38129.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067256 restraints weight = 41171.749| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 34364 Z= 0.227 Angle : 0.636 11.769 46942 Z= 0.317 Chirality : 0.044 0.232 5502 Planarity : 0.004 0.120 5902 Dihedral : 6.936 82.179 6198 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.23 % Favored : 92.52 % Rotamer: Outliers : 1.22 % Allowed : 14.70 % Favored : 84.08 % 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: -1.15 (0.13), residues: 4106 helix: 2.33 (0.21), residues: 624 sheet: -0.47 (0.16), residues: 1045 loop : -1.83 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 66 TYR 0.034 0.001 TYR A 904 PHE 0.030 0.001 PHE C 855 TRP 0.020 0.001 TRP C 104 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00529 (34227) covalent geometry : angle 0.62308 (46584) SS BOND : bond 0.00373 ( 53) SS BOND : angle 1.38295 ( 106) hydrogen bonds : bond 0.05040 ( 1006) hydrogen bonds : angle 4.94092 ( 2778) link_ALPHA1-3 : bond 0.00820 ( 3) link_ALPHA1-3 : angle 1.34474 ( 9) link_ALPHA1-6 : bond 0.00965 ( 3) link_ALPHA1-6 : angle 1.75267 ( 9) link_BETA1-4 : bond 0.00377 ( 29) link_BETA1-4 : angle 1.56405 ( 87) link_NAG-ASN : bond 0.00319 ( 49) link_NAG-ASN : angle 1.78256 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7688.70 seconds wall clock time: 132 minutes 39.29 seconds (7959.29 seconds total)