Starting phenix.real_space_refine on Sat Jul 4 11:49:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ks_67779/07_2026/21ks_67779.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ks_67779/07_2026/21ks_67779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21ks_67779/07_2026/21ks_67779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ks_67779/07_2026/21ks_67779.map" model { file = "/net/cci-nas-00/data/ceres_data/21ks_67779/07_2026/21ks_67779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ks_67779/07_2026/21ks_67779.cif" } resolution = 3.01 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 50 atoms to isotropic. 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 167 5.16 5 C 12456 2.51 5 N 3496 2.21 5 O 3751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19870 Number of models: 1 Model: "" Number of chains: 16 Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 947 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 12, 'TRANS': 105} Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 12, 'TRANS': 104} Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 959 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "A" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 317} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4903 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 23, 'TRANS': 592} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4903 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 23, 'TRANS': 592} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'RAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.77, per 1000 atoms: 0.19 Number of scatterers: 19870 At special positions: 0 Unit cell: (128.96, 133.952, 188.032, 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 167 16.00 O 3751 8.00 N 3496 7.00 C 12456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 118 " distance=2.04 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 118 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 111 " - pdb=" SG CYS G 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 118 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 80 " - pdb=" SG CYS H 118 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.04 Simple disulfide: pdb=" SG CYS B 893 " - pdb=" SG CYS B 904 " distance=2.03 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 914 " distance=2.03 Simple disulfide: pdb=" SG CYS B 916 " - pdb=" SG CYS B 929 " distance=2.03 Simple disulfide: pdb=" SG CYS B1207 " - pdb=" SG CYS B1218 " distance=2.03 Simple disulfide: pdb=" SG CYS B1214 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1230 " - pdb=" SG CYS B1243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 56 " distance=2.03 Simple disulfide: pdb=" SG CYS E 77 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 217 " distance=2.05 Simple disulfide: pdb=" SG CYS E 205 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 312 " distance=2.03 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 307 " distance=2.03 Simple disulfide: pdb=" SG CYS E 311 " - pdb=" SG CYS E 351 " distance=2.03 Simple disulfide: pdb=" SG CYS E 327 " - pdb=" SG CYS E 342 " distance=2.04 Simple disulfide: pdb=" SG CYS E 329 " - pdb=" SG CYS E 339 " distance=2.03 Simple disulfide: pdb=" SG CYS F 893 " - pdb=" SG CYS F 904 " distance=2.03 Simple disulfide: pdb=" SG CYS F 900 " - pdb=" SG CYS F 914 " distance=2.03 Simple disulfide: pdb=" SG CYS F 916 " - pdb=" SG CYS F 929 " distance=2.03 Simple disulfide: pdb=" SG CYS F1207 " - pdb=" SG CYS F1218 " distance=2.03 Simple disulfide: pdb=" SG CYS F1214 " - pdb=" SG CYS F1228 " distance=2.03 Simple disulfide: pdb=" SG CYS F1230 " - pdb=" SG CYS F1243 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 401 " - " ASN A 87 " " NAG B1501 " - " ASN B 859 " " NAG J 1 " - " ASN A 298 " " NAG K 1 " - " ASN B 692 " " NAG L 1 " - " ASN E 87 " " NAG M 1 " - " ASN E 298 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 814.6 milliseconds 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4618 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 20.6% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.714A pdb=" N GLU C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.972A pdb=" N LEU C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR C 93 " --> pdb=" O CYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 removed outlier: 3.768A pdb=" N CYS C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.578A pdb=" N MET C 122 " --> pdb=" O CYS C 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 removed outlier: 3.631A pdb=" N LYS G 44 " --> pdb=" O PRO G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 71 removed outlier: 3.956A pdb=" N ALA G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 82 through 93 removed outlier: 4.100A pdb=" N PHE G 86 " --> pdb=" O PRO G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 4.061A pdb=" N CYS G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.509A pdb=" N ALA D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.637A pdb=" N VAL D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 Processing helix chain 'D' and resid 107 through 123 removed outlier: 3.539A pdb=" N CYS D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLY D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Proline residue: D 120 - end of helix Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.520A pdb=" N ALA H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.554A pdb=" N VAL H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 93 removed outlier: 4.317A pdb=" N LYS H 85 " --> pdb=" O SER H 81 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE H 86 " --> pdb=" O PRO H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 removed outlier: 5.384A pdb=" N GLY H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 124 through 126 No H-bonds generated for 'chain 'H' and resid 124 through 126' Processing helix chain 'A' and resid 22 through 32 removed outlier: 6.279A pdb=" N GLY A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 49 through 59 Processing helix chain 'A' and resid 62 through 81 Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.790A pdb=" N VAL A 101 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 104 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 158 through 171 Processing helix chain 'A' and resid 178 through 197 removed outlier: 3.614A pdb=" N ILE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 1198 through 1204 removed outlier: 3.514A pdb=" N GLN B1204 " --> pdb=" O GLN B1200 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1214 Processing helix chain 'I' and resid 56 through 64 removed outlier: 3.659A pdb=" N ALA I 64 " --> pdb=" O GLU I 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 28 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 62 through 81 Processing helix chain 'E' and resid 98 through 103 removed outlier: 4.100A pdb=" N VAL E 101 " --> pdb=" O PHE E 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU E 102 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 Processing helix chain 'E' and resid 158 through 171 removed outlier: 3.602A pdb=" N GLY E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 197 removed outlier: 3.516A pdb=" N ALA E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 removed outlier: 3.557A pdb=" N GLY E 210 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 237 Processing helix chain 'E' and resid 306 through 311 removed outlier: 3.529A pdb=" N CYS E 311 " --> pdb=" O CYS E 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 900 removed outlier: 3.879A pdb=" N CYS F 900 " --> pdb=" O ASN F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 1198 through 1204 removed outlier: 3.743A pdb=" N GLN F1204 " --> pdb=" O GLN F1200 " (cutoff:3.500A) Processing helix chain 'F' and resid 1209 through 1214 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AA4, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 206 removed outlier: 3.820A pdb=" N VAL A 214 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 251 through 258 Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 297 removed outlier: 4.349A pdb=" N HIS A 349 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AA9, first strand: chain 'B' and resid 653 through 655 Processing sheet with id=AB1, first strand: chain 'B' and resid 664 through 670 removed outlier: 6.260A pdb=" N THR B 679 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU B 667 " --> pdb=" O TYR B 677 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR B 677 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE B 669 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B 675 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 686 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 707 through 713 removed outlier: 6.645A pdb=" N ILE B 729 " --> pdb=" O LEU B 742 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 750 through 756 removed outlier: 6.099A pdb=" N THR B 765 " --> pdb=" O ARG B 751 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 753 " --> pdb=" O TYR B 763 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR B 763 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU B 755 " --> pdb=" O PHE B 761 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE B 761 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 775 " --> pdb=" O THR B 785 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR B 785 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 793 through 799 removed outlier: 5.233A pdb=" N GLY B 795 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B 808 " --> pdb=" O GLY B 795 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER B 817 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 827 " --> pdb=" O SER B 817 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 835 through 841 removed outlier: 4.045A pdb=" N GLY B 837 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR B 848 " --> pdb=" O GLY B 837 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG B 857 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 868 " --> pdb=" O ARG B 857 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 905 through 907 removed outlier: 3.565A pdb=" N GLY B 911 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 921 through 922 Processing sheet with id=AB8, first strand: chain 'B' and resid 957 through 958 removed outlier: 6.744A pdb=" N PHE B 935 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA B1193 " --> pdb=" O PHE B 935 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 937 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE B1191 " --> pdb=" O LEU B 937 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N SER B 939 " --> pdb=" O SER B1189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 967 through 973 removed outlier: 4.022A pdb=" N ALA B 969 " --> pdb=" O ILE B 982 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 989 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1016 through 1018 removed outlier: 4.004A pdb=" N ASP B1018 " --> pdb=" O THR B1031 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1016 through 1018 removed outlier: 4.004A pdb=" N ASP B1018 " --> pdb=" O THR B1031 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1059 through 1065 removed outlier: 5.977A pdb=" N LEU B1076 " --> pdb=" O PRO B1059 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B1061 " --> pdb=" O THR B1074 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B1083 " --> pdb=" O LEU B1096 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1104 through 1110 removed outlier: 3.611A pdb=" N ALA B1106 " --> pdb=" O ALA B1119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B1119 " --> pdb=" O ALA B1106 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B1126 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1147 through 1153 removed outlier: 3.812A pdb=" N GLY B1149 " --> pdb=" O ILE B1160 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B1160 " --> pdb=" O GLY B1149 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B1167 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1217 through 1221 Processing sheet with id=AC7, first strand: chain 'I' and resid 37 through 38 removed outlier: 3.798A pdb=" N ASP I 37 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR I 21 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU I 106 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL I 23 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG I 71 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR I 6 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU E 341 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 13.772A pdb=" N SER I 8 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 17.597A pdb=" N CYS E 339 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS E 349 " --> pdb=" O CYS E 297 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 46 through 49 removed outlier: 6.078A pdb=" N THR I 21 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU I 106 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL I 23 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG I 71 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR I 6 " --> pdb=" O GLU E 341 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLU E 341 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 13.772A pdb=" N SER I 8 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 17.597A pdb=" N CYS E 339 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN E 340 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N HIS E 328 " --> pdb=" O GLN E 340 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N CYS E 342 " --> pdb=" O LYS E 326 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS E 326 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG E 344 " --> pdb=" O ARG E 324 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ARG E 324 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR E 346 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG E 322 " --> pdb=" O TYR E 346 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 348 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR E 320 " --> pdb=" O VAL E 348 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR E 350 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA E 318 " --> pdb=" O THR E 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 200 through 206 removed outlier: 3.743A pdb=" N HIS E 206 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL E 214 " --> pdb=" O HIS E 206 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 252 through 258 Processing sheet with id=AD2, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AD3, first strand: chain 'F' and resid 653 through 655 removed outlier: 3.564A pdb=" N PHE F 633 " --> pdb=" O PHE F 882 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 664 through 670 removed outlier: 4.201A pdb=" N ALA F 666 " --> pdb=" O THR F 679 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE F 686 " --> pdb=" O VAL F 699 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 707 through 713 removed outlier: 6.736A pdb=" N ILE F 729 " --> pdb=" O LEU F 742 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 754 through 756 removed outlier: 6.713A pdb=" N ILE F 773 " --> pdb=" O LEU F 786 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 793 through 799 removed outlier: 5.433A pdb=" N GLY F 795 " --> pdb=" O THR F 808 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR F 808 " --> pdb=" O GLY F 795 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER F 817 " --> pdb=" O VAL F 827 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL F 827 " --> pdb=" O SER F 817 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 835 through 841 removed outlier: 3.898A pdb=" N GLY F 837 " --> pdb=" O THR F 848 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR F 848 " --> pdb=" O GLY F 837 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE F 855 " --> pdb=" O ILE F 869 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 905 through 907 Processing sheet with id=AE1, first strand: chain 'F' and resid 921 through 922 Processing sheet with id=AE2, first strand: chain 'F' and resid 957 through 958 Processing sheet with id=AE3, first strand: chain 'F' and resid 971 through 973 removed outlier: 6.654A pdb=" N ILE F 989 " --> pdb=" O VAL F1002 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 1016 through 1022 removed outlier: 4.181A pdb=" N ASP F1018 " --> pdb=" O THR F1031 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 1059 through 1065 removed outlier: 5.840A pdb=" N LEU F1076 " --> pdb=" O PRO F1059 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA F1061 " --> pdb=" O THR F1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE F1083 " --> pdb=" O LEU F1096 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 1104 through 1110 removed outlier: 3.771A pdb=" N ALA F1106 " --> pdb=" O ALA F1119 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE F1126 " --> pdb=" O LEU F1139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 1147 through 1153 removed outlier: 4.092A pdb=" N GLY F1149 " --> pdb=" O ILE F1160 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS F1169 " --> pdb=" O LYS F1180 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS F1180 " --> pdb=" O LYS F1169 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASP F1171 " --> pdb=" O ARG F1178 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG F1178 " --> pdb=" O ASP F1171 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 1217 through 1221 Processing sheet with id=AE9, first strand: chain 'F' and resid 1235 through 1236 removed outlier: 3.833A pdb=" N VAL F1235 " --> pdb=" O GLY F1244 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F1244 " --> pdb=" O VAL F1235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 719 hydrogen bonds defined for protein. 1836 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: 3.56 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6640 1.34 - 1.48: 5060 1.48 - 1.61: 8424 1.61 - 1.74: 0 1.74 - 1.87: 224 Bond restraints: 20348 Sorted by residual: bond pdb=" C1 RAP I 201 " pdb=" O1 RAP I 201 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C8 RAP I 201 " pdb=" C9 RAP I 201 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CA SER A 338 " pdb=" C SER A 338 " ideal model delta sigma weight residual 1.521 1.557 -0.036 1.20e-02 6.94e+03 8.85e+00 bond pdb=" N CYS A 339 " pdb=" CA CYS A 339 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" C LYS G 102 " pdb=" N PRO G 103 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.01e-02 9.80e+03 6.89e+00 ... (remaining 20343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 26964 2.03 - 4.05: 512 4.05 - 6.08: 84 6.08 - 8.10: 27 8.10 - 10.13: 10 Bond angle restraints: 27597 Sorted by residual: angle pdb=" N CYS A 203 " pdb=" CA CYS A 203 " pdb=" C CYS A 203 " ideal model delta sigma weight residual 108.19 117.15 -8.96 1.29e+00 6.01e-01 4.83e+01 angle pdb=" N CYS E 203 " pdb=" CA CYS E 203 " pdb=" C CYS E 203 " ideal model delta sigma weight residual 108.45 115.70 -7.25 1.26e+00 6.30e-01 3.31e+01 angle pdb=" C GLU E 148 " pdb=" CA GLU E 148 " pdb=" CB GLU E 148 " ideal model delta sigma weight residual 116.54 110.28 6.26 1.15e+00 7.56e-01 2.96e+01 angle pdb=" C SER F1006 " pdb=" CA SER F1006 " pdb=" CB SER F1006 " ideal model delta sigma weight residual 116.54 110.37 6.17 1.15e+00 7.56e-01 2.87e+01 angle pdb=" C ASN B1065 " pdb=" N PRO B1066 " pdb=" CA PRO B1066 " ideal model delta sigma weight residual 119.56 114.40 5.16 1.01e+00 9.80e-01 2.61e+01 ... (remaining 27592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.47: 11262 26.47 - 52.93: 1144 52.93 - 79.40: 121 79.40 - 105.86: 40 105.86 - 132.33: 7 Dihedral angle restraints: 12574 sinusoidal: 5394 harmonic: 7180 Sorted by residual: dihedral pdb=" CA CYS E 334 " pdb=" C CYS E 334 " pdb=" N CYS E 335 " pdb=" CA CYS E 335 " ideal model delta harmonic sigma weight residual -180.00 -47.67 -132.33 0 5.00e+00 4.00e-02 7.00e+02 dihedral pdb=" CA TRP E 333 " pdb=" C TRP E 333 " pdb=" N CYS E 334 " pdb=" CA CYS E 334 " ideal model delta harmonic sigma weight residual -180.00 -71.35 -108.65 0 5.00e+00 4.00e-02 4.72e+02 dihedral pdb=" CA TRP A 333 " pdb=" C TRP A 333 " pdb=" N CYS A 334 " pdb=" CA CYS A 334 " ideal model delta harmonic sigma weight residual -180.00 -75.46 -104.54 0 5.00e+00 4.00e-02 4.37e+02 ... (remaining 12571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2455 0.058 - 0.116: 457 0.116 - 0.173: 54 0.173 - 0.231: 3 0.231 - 0.289: 1 Chirality restraints: 2970 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN E 87 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA CYS A 339 " pdb=" N CYS A 339 " pdb=" C CYS A 339 " pdb=" CB CYS A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C28 RAP I 201 " pdb=" C27 RAP I 201 " pdb=" C29 RAP I 201 " pdb=" O10 RAP I 201 " both_signs ideal model delta sigma weight residual False -2.29 -2.49 0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 2967 not shown) Planarity restraints: 3611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 337 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C VAL A 337 " -0.066 2.00e-02 2.50e+03 pdb=" O VAL A 337 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 338 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F1146 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO F1147 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO F1147 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F1147 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F1080 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO F1081 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO F1081 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F1081 " 0.046 5.00e-02 4.00e+02 ... (remaining 3608 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4708 2.79 - 3.32: 17957 3.32 - 3.84: 33966 3.84 - 4.37: 40120 4.37 - 4.90: 68412 Nonbonded interactions: 165163 Sorted by model distance: nonbonded pdb=" O SER F 896 " pdb=" OG SER F 896 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP B1089 " pdb=" OG1 THR B1091 " model vdw 2.261 3.040 nonbonded pdb=" NE1 TRP B 767 " pdb=" O ALA B 793 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR I 82 " pdb=" O3 RAP I 201 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR H 48 " pdb=" OG1 THR H 93 " model vdw 2.289 3.040 ... (remaining 165158 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 19 through 352) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 630 through 1245) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 33 through 149) selection = (chain 'D' and resid 33 through 149) selection = chain 'G' selection = (chain 'H' and resid 33 through 149) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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 individual isotropic 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.300 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 20412 Z= 0.189 Angle : 0.741 16.973 27735 Z= 0.397 Chirality : 0.046 0.289 2970 Planarity : 0.005 0.086 3605 Dihedral : 19.937 132.329 7794 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.63 % Allowed : 33.72 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.18), residues: 2462 helix: -0.03 (0.27), residues: 424 sheet: -0.83 (0.21), residues: 590 loop : -0.69 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B1046 TYR 0.033 0.002 TYR F 763 PHE 0.015 0.001 PHE C 87 TRP 0.050 0.002 TRP F1030 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (20348) covalent geometry : angle 0.72217 / 0.39 (27597) SS BOND : bond 0.00397 / 0.24 ( 54) SS BOND : angle 1.53905 / 0.95 ( 108) hydrogen bonds : bond 0.16083 / 10.55 ( 696) hydrogen bonds : angle 7.82903 / 5.40 ( 1836) link_BETA1-4 : bond 0.00852 / 0.43 ( 4) link_BETA1-4 : angle 2.22166 / 1.12 ( 12) link_NAG-ASN : bond 0.01093 / 0.78 ( 6) link_NAG-ASN : angle 5.34558 / 3.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 385 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 92 TYR cc_start: 0.7274 (m-80) cc_final: 0.6895 (m-80) REVERT: G 102 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6587 (ttpt) REVERT: G 122 MET cc_start: 0.2681 (tpp) cc_final: 0.2055 (tpp) REVERT: A 104 LYS cc_start: 0.7033 (mmtp) cc_final: 0.6809 (mtmm) REVERT: B 645 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6505 (pt) REVERT: B 687 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8697 (m) REVERT: B 779 ASP cc_start: 0.7608 (m-30) cc_final: 0.7386 (m-30) REVERT: B 841 TYR cc_start: 0.7495 (t80) cc_final: 0.6805 (t80) REVERT: B 965 ARG cc_start: 0.7407 (mtt-85) cc_final: 0.7203 (mtt90) REVERT: B 988 MET cc_start: 0.7642 (ptp) cc_final: 0.7430 (ptt) REVERT: B 1122 ASP cc_start: 0.6502 (t0) cc_final: 0.6292 (t0) REVERT: E 202 LYS cc_start: 0.6301 (mtpm) cc_final: 0.5938 (mttt) REVERT: E 286 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6849 (pm20) REVERT: F 985 ARG cc_start: 0.0322 (pmt170) cc_final: 0.0010 (tmm-80) REVERT: F 1118 TRP cc_start: 0.4431 (p90) cc_final: 0.3796 (p90) outliers start: 78 outliers final: 26 residues processed: 447 average time/residue: 0.1458 time to fit residues: 97.9909 Evaluate side-chains 286 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 909 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1080 SER Chi-restraints excluded: chain B residue 1121 SER Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain F residue 732 SER Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 942 SER Chi-restraints excluded: chain F residue 991 LYS Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 ASN B1182 GLN B1205 HIS B1211 ASN I 94 HIS E 188 ASN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 864 GLN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 998 GLN ** F1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.270616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.245177 restraints weight = 22757.799| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 1.31 r_work: 0.4426 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4349 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20412 Z= 0.207 Angle : 0.730 18.431 27735 Z= 0.368 Chirality : 0.049 0.341 2970 Planarity : 0.005 0.065 3605 Dihedral : 9.724 104.860 3107 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 6.05 % Allowed : 27.12 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.17), residues: 2462 helix: 0.00 (0.26), residues: 441 sheet: -0.82 (0.21), residues: 598 loop : -0.82 (0.18), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F1060 TYR 0.022 0.002 TYR A 32 PHE 0.018 0.002 PHE F 938 TRP 0.021 0.002 TRP F 678 HIS 0.006 0.001 HIS A 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (20348) covalent geometry : angle 0.70580 / 0.36 (27597) SS BOND : bond 0.00586 / 0.38 ( 54) SS BOND : angle 1.55145 / 1.11 ( 108) hydrogen bonds : bond 0.04375 / 2.82 ( 696) hydrogen bonds : angle 5.94601 / 4.09 ( 1836) link_BETA1-4 : bond 0.00632 / 0.31 ( 4) link_BETA1-4 : angle 2.66957 / 1.32 ( 12) link_NAG-ASN : bond 0.01559 / 0.91 ( 6) link_NAG-ASN : angle 6.18194 / 4.38 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 259 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.5014 (m-10) REVERT: B 945 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8407 (m-40) REVERT: B 968 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8137 (ptm160) REVERT: B 988 MET cc_start: 0.7730 (ptp) cc_final: 0.7459 (ptt) REVERT: B 990 ARG cc_start: 0.6970 (ttt90) cc_final: 0.6752 (ttt-90) REVERT: B 1026 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8286 (mmm160) REVERT: E 202 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.6031 (mttt) REVERT: E 322 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7233 (mmt180) REVERT: F 820 MET cc_start: 0.4736 (tpp) cc_final: 0.3785 (tpp) REVERT: F 985 ARG cc_start: 0.0812 (pmt170) cc_final: 0.0116 (tmm-80) REVERT: F 1071 MET cc_start: 0.5215 (ptp) cc_final: 0.4955 (ptp) REVERT: F 1118 TRP cc_start: 0.4807 (p90) cc_final: 0.4454 (p90) outliers start: 130 outliers final: 58 residues processed: 369 average time/residue: 0.1572 time to fit residues: 86.8831 Evaluate side-chains 281 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 720 TYR Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 779 ASP Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 885 SER Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1116 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 135 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 172 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN B 923 ASN I 53 GLN F 738 HIS ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.259618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.230481 restraints weight = 22438.456| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 1.45 r_work: 0.4265 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 20412 Z= 0.163 Angle : 0.639 17.624 27735 Z= 0.323 Chirality : 0.045 0.280 2970 Planarity : 0.004 0.046 3605 Dihedral : 8.564 103.965 3080 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 4.60 % Allowed : 27.49 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.95 (0.17), residues: 2462 helix: 0.23 (0.26), residues: 434 sheet: -0.72 (0.20), residues: 635 loop : -0.81 (0.18), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 852 TYR 0.016 0.001 TYR B1202 PHE 0.031 0.002 PHE B1000 TRP 0.020 0.001 TRP F 678 HIS 0.006 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (20348) covalent geometry : angle 0.61509 / 0.32 (27597) SS BOND : bond 0.00387 / 0.26 ( 54) SS BOND : angle 1.53218 / 1.07 ( 108) hydrogen bonds : bond 0.03979 / 2.55 ( 696) hydrogen bonds : angle 5.70116 / 3.92 ( 1836) link_BETA1-4 : bond 0.01324 / 0.66 ( 4) link_BETA1-4 : angle 2.59255 / 1.30 ( 12) link_NAG-ASN : bond 0.01076 / 0.71 ( 6) link_NAG-ASN : angle 5.49944 / 4.05 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 238 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5437 (p90) REVERT: H 53 MET cc_start: 0.2712 (ttt) cc_final: 0.2248 (mmm) REVERT: A 138 CYS cc_start: 0.7681 (m) cc_final: 0.7282 (m) REVERT: B 820 MET cc_start: 0.8489 (mmt) cc_final: 0.8283 (mmt) REVERT: B 841 TYR cc_start: 0.8160 (t80) cc_final: 0.7919 (t80) REVERT: B 945 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8099 (m110) REVERT: B 968 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8152 (ptm160) REVERT: B 988 MET cc_start: 0.7721 (ptp) cc_final: 0.7403 (ptt) REVERT: I 25 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.7244 (t-90) REVERT: E 322 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7249 (mmt180) REVERT: F 961 ILE cc_start: 0.7354 (mp) cc_final: 0.7123 (mp) REVERT: F 985 ARG cc_start: 0.0261 (pmt170) cc_final: -0.0099 (tmm-80) REVERT: F 1071 MET cc_start: 0.5025 (ptp) cc_final: 0.4721 (ptp) REVERT: F 1232 MET cc_start: 0.1736 (mpp) cc_final: 0.1153 (mmm) outliers start: 99 outliers final: 56 residues processed: 317 average time/residue: 0.1513 time to fit residues: 72.8845 Evaluate side-chains 271 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1085 ARG Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 975 LEU Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 116 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 226 optimal weight: 30.0000 chunk 239 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN B 902 HIS B 923 ASN E 221 GLN E 349 HIS F 902 HIS ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1075 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.254378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.220442 restraints weight = 22015.795| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.59 r_work: 0.4145 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 20412 Z= 0.378 Angle : 0.810 20.543 27735 Z= 0.405 Chirality : 0.052 0.352 2970 Planarity : 0.006 0.061 3605 Dihedral : 8.496 104.322 3076 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 6.60 % Allowed : 25.16 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.31 (0.17), residues: 2462 helix: -0.22 (0.25), residues: 434 sheet: -0.81 (0.20), residues: 629 loop : -1.06 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.022 0.002 TYR E 59 PHE 0.021 0.003 PHE B 882 TRP 0.030 0.002 TRP F1118 HIS 0.010 0.001 HIS A 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.38 (20348) covalent geometry : angle 0.78175 / 0.40 (27597) SS BOND : bond 0.00644 / 0.38 ( 54) SS BOND : angle 1.89746 / 1.36 ( 108) hydrogen bonds : bond 0.04963 / 3.14 ( 696) hydrogen bonds : angle 6.12859 / 4.21 ( 1836) link_BETA1-4 : bond 0.00925 / 0.47 ( 4) link_BETA1-4 : angle 3.20867 / 1.62 ( 12) link_NAG-ASN : bond 0.01926 / 1.03 ( 6) link_NAG-ASN : angle 6.82028 / 4.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 232 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5631 (p90) REVERT: C 122 MET cc_start: 0.2319 (mtt) cc_final: 0.1999 (ttp) REVERT: A 157 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 174 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: A 178 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: A 223 ASP cc_start: 0.7396 (t0) cc_final: 0.7194 (t0) REVERT: A 347 ASP cc_start: 0.6574 (p0) cc_final: 0.6252 (p0) REVERT: B 806 TYR cc_start: 0.8543 (m-80) cc_final: 0.8293 (m-80) REVERT: B 820 MET cc_start: 0.8700 (mmt) cc_final: 0.8303 (mmt) REVERT: B 841 TYR cc_start: 0.8362 (t80) cc_final: 0.8060 (t80) REVERT: B 945 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8809 (m-40) REVERT: B 968 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7761 (ptp90) REVERT: B 988 MET cc_start: 0.7951 (ptp) cc_final: 0.7568 (ptt) REVERT: I 25 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7546 (t-90) REVERT: E 174 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: E 263 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6179 (m-80) REVERT: E 270 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: E 322 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7424 (mmt90) outliers start: 142 outliers final: 82 residues processed: 351 average time/residue: 0.1426 time to fit residues: 75.3007 Evaluate side-chains 300 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 207 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1044 ASP Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1007 VAL Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1170 ILE Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 96 optimal weight: 0.0270 chunk 233 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 154 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 overall best weight: 2.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN B 653 ASN B1198 ASN B1205 HIS ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.255445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.236391 restraints weight = 22197.052| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 0.87 r_work: 0.4276 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.4222 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.4107 rms_B_bonded: 3.96 restraints_weight: 0.1250 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 20412 Z= 0.305 Angle : 0.727 19.319 27735 Z= 0.364 Chirality : 0.049 0.293 2970 Planarity : 0.005 0.050 3605 Dihedral : 8.276 107.606 3075 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 5.30 % Allowed : 26.37 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.39 (0.17), residues: 2462 helix: -0.19 (0.25), residues: 446 sheet: -0.97 (0.19), residues: 632 loop : -1.11 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 319 TYR 0.041 0.002 TYR F1072 PHE 0.022 0.002 PHE F 938 TRP 0.031 0.002 TRP F1118 HIS 0.010 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.30 (20348) covalent geometry : angle 0.69953 / 0.36 (27597) SS BOND : bond 0.00518 / 0.32 ( 54) SS BOND : angle 1.75673 / 1.25 ( 108) hydrogen bonds : bond 0.04394 / 2.79 ( 696) hydrogen bonds : angle 5.98887 / 4.09 ( 1836) link_BETA1-4 : bond 0.00914 / 0.46 ( 4) link_BETA1-4 : angle 3.33704 / 1.68 ( 12) link_NAG-ASN : bond 0.01597 / 0.87 ( 6) link_NAG-ASN : angle 6.18887 / 4.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 221 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5430 (p90) REVERT: H 53 MET cc_start: 0.2563 (ttt) cc_final: 0.2089 (mmm) REVERT: A 107 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7612 (mtp180) REVERT: A 157 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: B 706 TYR cc_start: 0.8550 (t80) cc_final: 0.8276 (t80) REVERT: B 820 MET cc_start: 0.8734 (mmt) cc_final: 0.8484 (mmt) REVERT: B 841 TYR cc_start: 0.8271 (t80) cc_final: 0.7964 (t80) REVERT: B 945 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8780 (m-40) REVERT: B 968 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7739 (ptp90) REVERT: B 988 MET cc_start: 0.8061 (ptp) cc_final: 0.7727 (ptt) REVERT: B 1157 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8950 (tp) REVERT: I 25 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7574 (t-90) REVERT: E 174 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: E 263 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: E 322 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7517 (mmt90) REVERT: F 751 ARG cc_start: 0.6587 (tpt90) cc_final: 0.6343 (tpt90) REVERT: F 820 MET cc_start: 0.4802 (tpp) cc_final: 0.4447 (tpp) REVERT: F 1232 MET cc_start: 0.1700 (mpp) cc_final: 0.1222 (mmm) outliers start: 114 outliers final: 79 residues processed: 317 average time/residue: 0.1409 time to fit residues: 67.1321 Evaluate side-chains 293 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 204 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1044 ASP Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 25 HIS Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 20 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 747 LEU Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1132 SER Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1170 ILE Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 150 optimal weight: 0.0470 chunk 182 optimal weight: 20.0000 chunk 104 optimal weight: 0.0060 chunk 9 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B1198 ASN B1205 HIS ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.257697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.238737 restraints weight = 22164.670| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 0.88 r_work: 0.4278 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.4225 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.4115 rms_B_bonded: 3.84 restraints_weight: 0.1250 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20412 Z= 0.142 Angle : 0.632 17.389 27735 Z= 0.315 Chirality : 0.045 0.259 2970 Planarity : 0.004 0.040 3605 Dihedral : 7.941 108.129 3075 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 5.12 % Allowed : 26.37 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2462 helix: 0.23 (0.25), residues: 446 sheet: -0.87 (0.19), residues: 616 loop : -0.98 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 852 TYR 0.019 0.001 TYR F1072 PHE 0.023 0.001 PHE B1000 TRP 0.033 0.001 TRP F1118 HIS 0.009 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (20348) covalent geometry : angle 0.60674 / 0.31 (27597) SS BOND : bond 0.00402 / 0.22 ( 54) SS BOND : angle 1.52712 / 1.07 ( 108) hydrogen bonds : bond 0.03596 / 2.32 ( 696) hydrogen bonds : angle 5.68489 / 3.89 ( 1836) link_BETA1-4 : bond 0.00850 / 0.43 ( 4) link_BETA1-4 : angle 2.94156 / 1.48 ( 12) link_NAG-ASN : bond 0.01066 / 0.72 ( 6) link_NAG-ASN : angle 5.53366 / 4.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 232 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.5728 (p90) REVERT: H 53 MET cc_start: 0.2473 (ttt) cc_final: 0.2011 (mmm) REVERT: A 157 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: A 174 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: A 223 ASP cc_start: 0.7154 (t0) cc_final: 0.6952 (t0) REVERT: B 706 TYR cc_start: 0.8396 (t80) cc_final: 0.8135 (t80) REVERT: B 841 TYR cc_start: 0.8171 (t80) cc_final: 0.7910 (t80) REVERT: B 945 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8223 (m110) REVERT: B 968 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7516 (ptp90) REVERT: B 988 MET cc_start: 0.7979 (ptp) cc_final: 0.7636 (ptt) REVERT: B 1157 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8925 (tp) REVERT: E 263 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: E 322 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7457 (mmt180) REVERT: F 947 MET cc_start: 0.7499 (mtm) cc_final: 0.7281 (mtm) REVERT: F 1184 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6454 (mmm160) REVERT: F 1232 MET cc_start: 0.1444 (mpp) cc_final: 0.1238 (mmm) outliers start: 110 outliers final: 79 residues processed: 320 average time/residue: 0.1399 time to fit residues: 67.4767 Evaluate side-chains 302 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 214 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 680 ASP Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 691 MET Chi-restraints excluded: chain F residue 747 LEU Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 945 ASN Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1116 LEU Chi-restraints excluded: chain F residue 1145 LEU Chi-restraints excluded: chain F residue 1184 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 207 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 0.0870 chunk 215 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 HIS I 25 HIS E 221 GLN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.257866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.232303 restraints weight = 22186.379| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 1.24 r_work: 0.4299 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20412 Z= 0.136 Angle : 0.625 17.168 27735 Z= 0.311 Chirality : 0.044 0.264 2970 Planarity : 0.004 0.038 3605 Dihedral : 7.721 106.681 3075 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 4.70 % Allowed : 27.44 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2462 helix: 0.43 (0.26), residues: 436 sheet: -0.80 (0.20), residues: 616 loop : -0.89 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1046 TYR 0.013 0.001 TYR E 336 PHE 0.023 0.001 PHE C 87 TRP 0.026 0.001 TRP F1118 HIS 0.009 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (20348) covalent geometry : angle 0.60141 / 0.30 (27597) SS BOND : bond 0.00337 / 0.21 ( 54) SS BOND : angle 1.49806 / 1.06 ( 108) hydrogen bonds : bond 0.03503 / 2.25 ( 696) hydrogen bonds : angle 5.55068 / 3.80 ( 1836) link_BETA1-4 : bond 0.00818 / 0.41 ( 4) link_BETA1-4 : angle 2.72952 / 1.38 ( 12) link_NAG-ASN : bond 0.01094 / 0.74 ( 6) link_NAG-ASN : angle 5.42412 / 3.96 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 230 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.4974 (p90) REVERT: D 91 MET cc_start: 0.5500 (tmm) cc_final: 0.5177 (tmm) REVERT: H 53 MET cc_start: 0.2368 (ttt) cc_final: 0.1994 (mmm) REVERT: H 149 MET cc_start: 0.2809 (ttp) cc_final: 0.2417 (mmm) REVERT: A 157 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: A 174 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: B 706 TYR cc_start: 0.8277 (t80) cc_final: 0.8046 (t80) REVERT: B 841 TYR cc_start: 0.8057 (t80) cc_final: 0.7824 (t80) REVERT: B 874 ASP cc_start: 0.7124 (t0) cc_final: 0.6903 (t0) REVERT: B 945 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8141 (m110) REVERT: B 968 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7426 (ptp90) REVERT: B 988 MET cc_start: 0.7797 (ptp) cc_final: 0.7479 (ptt) REVERT: B 1166 MET cc_start: 0.8038 (mtp) cc_final: 0.7773 (mmt) REVERT: I 79 ASP cc_start: 0.5954 (t0) cc_final: 0.5741 (t0) REVERT: E 263 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: F 820 MET cc_start: 0.4073 (tpp) cc_final: 0.3580 (tpp) REVERT: F 1184 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6473 (mmm160) outliers start: 101 outliers final: 77 residues processed: 309 average time/residue: 0.1398 time to fit residues: 65.0825 Evaluate side-chains 304 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 220 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 658 LEU Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 691 MET Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1116 LEU Chi-restraints excluded: chain F residue 1184 ARG Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 232 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 ASN B1205 HIS E 187 ASN ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.260628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.242904 restraints weight = 22074.358| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 0.85 r_work: 0.4336 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4278 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.4186 rms_B_bonded: 3.62 restraints_weight: 0.1250 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 20412 Z= 0.135 Angle : 0.624 17.088 27735 Z= 0.308 Chirality : 0.044 0.270 2970 Planarity : 0.004 0.038 3605 Dihedral : 7.589 105.436 3075 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 4.70 % Allowed : 27.44 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.17), residues: 2462 helix: 0.52 (0.26), residues: 435 sheet: -0.75 (0.19), residues: 630 loop : -0.89 (0.18), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 852 TYR 0.013 0.001 TYR E 336 PHE 0.022 0.001 PHE B1000 TRP 0.029 0.001 TRP F1118 HIS 0.008 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (20348) covalent geometry : angle 0.60014 / 0.30 (27597) SS BOND : bond 0.00442 / 0.26 ( 54) SS BOND : angle 1.52909 / 1.08 ( 108) hydrogen bonds : bond 0.03463 / 2.22 ( 696) hydrogen bonds : angle 5.49318 / 3.76 ( 1836) link_BETA1-4 : bond 0.00825 / 0.41 ( 4) link_BETA1-4 : angle 2.58822 / 1.31 ( 12) link_NAG-ASN : bond 0.01083 / 0.74 ( 6) link_NAG-ASN : angle 5.36222 / 3.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 234 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5623 (p90) REVERT: C 133 MET cc_start: 0.2576 (ptt) cc_final: 0.2034 (tpt) REVERT: H 149 MET cc_start: 0.2985 (ttp) cc_final: 0.2483 (mmm) REVERT: A 157 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: A 174 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: A 223 ASP cc_start: 0.7305 (t0) cc_final: 0.6982 (t0) REVERT: A 347 ASP cc_start: 0.6573 (t0) cc_final: 0.6313 (t0) REVERT: B 706 TYR cc_start: 0.8324 (t80) cc_final: 0.8054 (t80) REVERT: B 841 TYR cc_start: 0.8085 (t80) cc_final: 0.7787 (t80) REVERT: B 874 ASP cc_start: 0.7121 (t0) cc_final: 0.6918 (t0) REVERT: B 945 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: B 968 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7525 (ptp90) REVERT: B 988 MET cc_start: 0.7995 (ptp) cc_final: 0.7686 (ptt) REVERT: E 263 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: F 820 MET cc_start: 0.4101 (tpp) cc_final: 0.3280 (tpp) REVERT: F 1184 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6502 (mmm160) outliers start: 101 outliers final: 78 residues processed: 313 average time/residue: 0.1474 time to fit residues: 69.4404 Evaluate side-chains 306 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 221 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 945 ASN Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 686 ILE Chi-restraints excluded: chain F residue 691 MET Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1116 LEU Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1173 THR Chi-restraints excluded: chain F residue 1184 ARG Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 201 optimal weight: 0.0040 chunk 223 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 HIS ** E 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.258848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.239619 restraints weight = 22072.907| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 0.90 r_work: 0.4409 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.4370 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20412 Z= 0.130 Angle : 0.623 16.951 27735 Z= 0.306 Chirality : 0.044 0.275 2970 Planarity : 0.004 0.039 3605 Dihedral : 7.477 104.089 3075 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 4.09 % Allowed : 28.23 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.91 (0.17), residues: 2462 helix: 0.59 (0.26), residues: 435 sheet: -0.76 (0.20), residues: 644 loop : -0.87 (0.18), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 54 TYR 0.013 0.001 TYR E 336 PHE 0.023 0.001 PHE B1000 TRP 0.034 0.001 TRP F1118 HIS 0.008 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (20348) covalent geometry : angle 0.60028 / 0.30 (27597) SS BOND : bond 0.00382 / 0.23 ( 54) SS BOND : angle 1.47246 / 1.04 ( 108) hydrogen bonds : bond 0.03369 / 2.15 ( 696) hydrogen bonds : angle 5.40466 / 3.71 ( 1836) link_BETA1-4 : bond 0.00732 / 0.37 ( 4) link_BETA1-4 : angle 2.44445 / 1.24 ( 12) link_NAG-ASN : bond 0.01076 / 0.74 ( 6) link_NAG-ASN : angle 5.29594 / 3.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 225 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.5782 (OUTLIER) cc_final: 0.5298 (p90) REVERT: C 133 MET cc_start: 0.2544 (ptt) cc_final: 0.2062 (tpt) REVERT: H 149 MET cc_start: 0.2938 (ttp) cc_final: 0.2546 (mmm) REVERT: A 157 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 174 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: A 223 ASP cc_start: 0.7150 (t0) cc_final: 0.6862 (t0) REVERT: A 294 ASP cc_start: 0.7591 (m-30) cc_final: 0.7260 (m-30) REVERT: A 347 ASP cc_start: 0.6223 (t0) cc_final: 0.6015 (t0) REVERT: B 706 TYR cc_start: 0.8262 (t80) cc_final: 0.7939 (t80) REVERT: B 841 TYR cc_start: 0.7953 (t80) cc_final: 0.7699 (t80) REVERT: B 968 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7933 (ptm160) REVERT: B 988 MET cc_start: 0.7758 (ptp) cc_final: 0.7486 (ptt) REVERT: E 263 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: E 270 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: F 820 MET cc_start: 0.3938 (tpp) cc_final: 0.3166 (tpp) REVERT: F 1184 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6520 (mmm160) outliers start: 88 outliers final: 76 residues processed: 298 average time/residue: 0.1450 time to fit residues: 65.7322 Evaluate side-chains 300 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 691 MET Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1007 VAL Chi-restraints excluded: chain F residue 1116 LEU Chi-restraints excluded: chain F residue 1132 SER Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1173 THR Chi-restraints excluded: chain F residue 1184 ARG Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 88 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 ASN B1205 HIS E 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.260269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.241437 restraints weight = 22078.637| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 0.89 r_work: 0.4303 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.4252 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20412 Z= 0.146 Angle : 0.633 17.166 27735 Z= 0.312 Chirality : 0.044 0.279 2970 Planarity : 0.004 0.040 3605 Dihedral : 7.457 103.326 3075 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 4.42 % Allowed : 27.63 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.90 (0.17), residues: 2462 helix: 0.61 (0.26), residues: 435 sheet: -0.74 (0.19), residues: 644 loop : -0.88 (0.18), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.014 0.001 TYR E 336 PHE 0.024 0.001 PHE B1000 TRP 0.040 0.001 TRP F1118 HIS 0.008 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (20348) covalent geometry : angle 0.61009 / 0.31 (27597) SS BOND : bond 0.00426 / 0.25 ( 54) SS BOND : angle 1.47598 / 1.04 ( 108) hydrogen bonds : bond 0.03482 / 2.24 ( 696) hydrogen bonds : angle 5.39491 / 3.70 ( 1836) link_BETA1-4 : bond 0.00785 / 0.39 ( 4) link_BETA1-4 : angle 2.42096 / 1.22 ( 12) link_NAG-ASN : bond 0.01130 / 0.75 ( 6) link_NAG-ASN : angle 5.39185 / 3.94 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4924 Ramachandran restraints generated. 2462 Oldfield, 0 Emsley, 2462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 227 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5307 (p90) REVERT: H 149 MET cc_start: 0.2875 (ttp) cc_final: 0.2556 (mmm) REVERT: A 174 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: A 223 ASP cc_start: 0.6922 (t0) cc_final: 0.6644 (t0) REVERT: B 706 TYR cc_start: 0.8325 (t80) cc_final: 0.7984 (t80) REVERT: B 841 TYR cc_start: 0.8038 (t80) cc_final: 0.7737 (t80) REVERT: B 968 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7897 (ptm160) REVERT: B 988 MET cc_start: 0.7750 (ptp) cc_final: 0.7460 (ptt) REVERT: B 1166 MET cc_start: 0.7971 (mtp) cc_final: 0.7698 (mmt) REVERT: E 263 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6084 (m-80) REVERT: E 270 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: F 820 MET cc_start: 0.4101 (tpp) cc_final: 0.3261 (tpp) REVERT: F 1118 TRP cc_start: 0.3768 (p90) cc_final: 0.3439 (p90) REVERT: F 1184 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6547 (mmm160) outliers start: 95 outliers final: 82 residues processed: 304 average time/residue: 0.1340 time to fit residues: 62.0168 Evaluate side-chains 304 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 216 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain A residue 20 TYR Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 814 LEU Chi-restraints excluded: chain B residue 820 MET Chi-restraints excluded: chain B residue 828 ILE Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 934 THR Chi-restraints excluded: chain B residue 936 LEU Chi-restraints excluded: chain B residue 947 MET Chi-restraints excluded: chain B residue 954 SER Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 971 ASP Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1137 ILE Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1215 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 87 HIS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 263 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 681 ILE Chi-restraints excluded: chain F residue 691 MET Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain F residue 763 TYR Chi-restraints excluded: chain F residue 797 THR Chi-restraints excluded: chain F residue 814 LEU Chi-restraints excluded: chain F residue 827 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 832 LEU Chi-restraints excluded: chain F residue 839 THR Chi-restraints excluded: chain F residue 861 THR Chi-restraints excluded: chain F residue 879 ILE Chi-restraints excluded: chain F residue 979 LEU Chi-restraints excluded: chain F residue 1007 VAL Chi-restraints excluded: chain F residue 1105 ILE Chi-restraints excluded: chain F residue 1116 LEU Chi-restraints excluded: chain F residue 1132 SER Chi-restraints excluded: chain F residue 1148 VAL Chi-restraints excluded: chain F residue 1173 THR Chi-restraints excluded: chain F residue 1184 ARG Chi-restraints excluded: chain F residue 1219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 114 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 183 optimal weight: 0.0970 chunk 217 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 189 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1205 HIS E 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.260266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.241117 restraints weight = 22081.494| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 0.90 r_work: 0.4314 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work: 0.4170 rms_B_bonded: 3.56 restraints_weight: 0.1250 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20412 Z= 0.150 Angle : 0.640 17.207 27735 Z= 0.316 Chirality : 0.045 0.280 2970 Planarity : 0.004 0.038 3605 Dihedral : 7.472 103.379 3075 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 4.23 % Allowed : 27.95 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.89 (0.17), residues: 2462 helix: 0.61 (0.26), residues: 435 sheet: -0.70 (0.20), residues: 644 loop : -0.89 (0.18), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.013 0.001 TYR E 336 PHE 0.024 0.001 PHE B1000 TRP 0.036 0.001 TRP F1118 HIS 0.008 0.001 HIS B1233 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (20348) covalent geometry : angle 0.61793 / 0.31 (27597) SS BOND : bond 0.00408 / 0.25 ( 54) SS BOND : angle 1.48227 / 1.04 ( 108) hydrogen bonds : bond 0.03525 / 2.28 ( 696) hydrogen bonds : angle 5.41940 / 3.71 ( 1836) link_BETA1-4 : bond 0.00757 / 0.38 ( 4) link_BETA1-4 : angle 2.38926 / 1.21 ( 12) link_NAG-ASN : bond 0.01122 / 0.74 ( 6) link_NAG-ASN : angle 5.39880 / 3.95 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5556.21 seconds wall clock time: 95 minutes 36.73 seconds (5736.73 seconds total)