Starting phenix.real_space_refine on Sat Jul 4 16:37:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.map" model { file = "/net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uai_26426/07_2026/7uai_26426.cif" } resolution = 2.8 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= 0.003 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 S 111 5.16 5 C 13848 2.51 5 N 3637 2.21 5 O 4328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 106 residue(s): 0.02s 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: 21936 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4280 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2004 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 254} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 4, 'HIS:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4296 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 4250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4250 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4300 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2192 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 262} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.49, per 1000 atoms: 0.25 Number of scatterers: 21936 At special positions: 0 Unit cell: (125.786, 149.813, 161.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 111 16.00 O 4328 8.00 N 3637 7.00 C 13848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 259 " distance=2.02 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 147 " distance=2.01 Simple disulfide: pdb=" SG CYS E 269 " - pdb=" SG CYS E 277 " distance=2.02 Simple disulfide: pdb=" SG CYS E 343 " - pdb=" SG CYS E 431 " distance=2.03 Simple disulfide: pdb=" SG CYS E 557 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 36 " - pdb=" SG CYS A 368 " distance=2.06 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 104 " distance=2.07 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 137 " distance=2.05 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 254 " distance=2.06 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 259 " distance=2.02 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 147 " distance=1.99 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 277 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS D 308 " distance=2.02 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS B 559 " distance=2.04 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 259 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 147 " distance=1.99 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 277 " distance=2.02 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 431 " distance=2.02 Simple disulfide: pdb=" SG CYS C 557 " - pdb=" SG CYS C 559 " distance=2.04 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 259 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=1.99 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 277 " distance=2.00 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.00 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.04 Simple disulfide: pdb=" SG CYS H 36 " - pdb=" SG CYS H 368 " distance=2.06 Simple disulfide: pdb=" SG CYS H 93 " - pdb=" SG CYS H 104 " distance=2.06 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS H 137 " distance=2.04 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 154 " distance=2.03 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS H 254 " distance=2.06 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 F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " NAG R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " BETA1-6 " NAG I 1 " - " FUC I 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 4 " " NAG Q 1 " - " FUC Q 4 " " NAG T 1 " - " FUC T 4 " NAG-ASN " NAG B 704 " - " ASN B 440 " " NAG C 704 " - " ASN C 440 " " NAG D 703 " - " ASN D 440 " " NAG E 704 " - " ASN E 440 " " NAG F 1 " - " ASN E 258 " " NAG G 1 " - " ASN E 222 " " NAG I 1 " - " ASN E 414 " " NAG J 1 " - " ASN E 140 " " NAG K 1 " - " ASN B 140 " " NAG L 1 " - " ASN B 258 " " NAG M 1 " - " ASN B 222 " " NAG N 1 " - " ASN B 414 " " NAG O 1 " - " ASN C 140 " " NAG P 1 " - " ASN C 222 " " NAG Q 1 " - " ASN C 414 " " NAG R 1 " - " ASN D 258 " " NAG S 1 " - " ASN D 222 " " NAG T 1 " - " ASN D 414 " " NAG U 1 " - " ASN D 140 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS D 155 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS D 159 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 165 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 155 " pdb="ZN ZN B 702 " - pdb=" NE2 HIS B 159 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 165 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 159 " pdb="ZN ZN C 702 " - pdb=" NE2 HIS C 155 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 165 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 155 " pdb="ZN ZN E 702 " - pdb=" NE2 HIS E 159 " 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 48 sheets defined 23.1% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 88 through 106 Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 180 through 183 Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 232 through 238 Processing helix chain 'E' and resid 246 through 258 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 411 through 415 Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 516 through 520 Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'E' and resid 546 through 551 Processing helix chain 'E' and resid 573 through 577 Processing helix chain 'E' and resid 597 through 600 Processing helix chain 'A' and resid 38 through 56 removed outlier: 3.799A pdb=" N GLY A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 164 through 182 Processing helix chain 'A' and resid 342 through 345 removed outlier: 3.629A pdb=" N PHE A 345 " --> pdb=" O SER A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.609A pdb=" N LEU A 380 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 440 through 448 Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 546 through 551 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 578 through 581 removed outlier: 4.028A pdb=" N PHE B 581 " --> pdb=" O ARG B 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 581' Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 88 through 106 Processing helix chain 'C' and resid 149 through 162 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 180 through 183 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 234 through 239 removed outlier: 4.241A pdb=" N ILE C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 440 through 448 Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 546 through 551 Processing helix chain 'C' and resid 573 through 577 Processing helix chain 'C' and resid 597 through 600 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'D' and resid 180 through 183 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 493 through 497 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 546 through 551 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 597 through 600 Processing helix chain 'H' and resid 38 through 56 removed outlier: 3.574A pdb=" N ALA H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 108 through 111 Processing helix chain 'H' and resid 143 through 151 Processing helix chain 'H' and resid 164 through 182 Processing helix chain 'H' and resid 342 through 345 Processing helix chain 'H' and resid 360 through 364 Processing sheet with id=AA1, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'E' and resid 110 through 112 removed outlier: 7.996A pdb=" N PHE E 122 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 82 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.191A pdb=" N ASP E 423 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 12.047A pdb=" N TYR E 313 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 265 through 269 removed outlier: 5.700A pdb=" N LEU E 421 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS E 349 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP E 423 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE E 347 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 280 through 281 removed outlier: 6.285A pdb=" N VAL E 362 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS E 376 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG E 364 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU E 374 " --> pdb=" O ARG E 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'E' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'E' and resid 454 through 455 removed outlier: 6.204A pdb=" N LEU E 482 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AB2, first strand: chain 'A' and resid 32 through 33 removed outlier: 5.595A pdb=" N CYS A 93 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG A 63 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 91 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 65 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU A 89 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL A 67 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP A 87 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A 113 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TYR A 122 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU A 132 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN A 124 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 130 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 156 through 157 removed outlier: 6.549A pdb=" N LEU A 210 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL A 192 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU A 208 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG A 194 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 206 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER A 196 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A 204 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 235 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 156 through 157 removed outlier: 6.549A pdb=" N LEU A 210 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL A 192 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU A 208 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG A 194 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 206 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER A 196 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A 204 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 235 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB6, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 110 through 112 Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 269 Processing sheet with id=AC1, first strand: chain 'B' and resid 265 through 269 removed outlier: 5.763A pdb=" N LEU B 421 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 349 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP B 423 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE B 347 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 280 through 281 removed outlier: 5.914A pdb=" N VAL B 362 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS B 376 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG B 364 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU B 374 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 434 through 439 Processing sheet with id=AC4, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC5, first strand: chain 'B' and resid 454 through 455 removed outlier: 6.189A pdb=" N LEU B 482 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 569 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 552 through 554 Processing sheet with id=AC7, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC8, first strand: chain 'C' and resid 110 through 112 removed outlier: 7.881A pdb=" N PHE C 122 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 82 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AD1, first strand: chain 'C' and resid 265 through 269 Processing sheet with id=AD2, first strand: chain 'C' and resid 265 through 269 removed outlier: 5.602A pdb=" N LEU C 421 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LYS C 349 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP C 423 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE C 347 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.479A pdb=" N LEU C 358 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR C 379 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 360 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 434 through 438 Processing sheet with id=AD5, first strand: chain 'C' and resid 454 through 455 Processing sheet with id=AD6, first strand: chain 'C' and resid 454 through 455 removed outlier: 4.129A pdb=" N ILE C 571 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU C 484 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY C 569 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE C 486 " --> pdb=" O TRP C 567 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TRP C 567 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL C 488 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N LEU C 565 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 534 through 535 removed outlier: 3.683A pdb=" N THR C 541 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AD9, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AE1, first strand: chain 'D' and resid 110 through 112 removed outlier: 8.056A pdb=" N PHE D 122 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 82 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AE3, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.983A pdb=" N ASP D 423 " --> pdb=" O TYR D 313 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N TYR D 313 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.708A pdb=" N LEU D 421 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS D 349 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP D 423 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 347 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.093A pdb=" N VAL D 362 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS D 376 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU D 374 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 434 through 438 Processing sheet with id=AE7, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AE8, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.666A pdb=" N ILE D 571 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU D 484 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY D 569 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE D 486 " --> pdb=" O TRP D 567 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TRP D 567 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL D 488 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LEU D 565 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AF1, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.017A pdb=" N ALA H 70 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N CYS H 93 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG H 63 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR H 91 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN H 65 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU H 89 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL H 67 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASP H 87 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL H 113 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR H 122 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU H 132 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ASN H 124 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU H 130 " --> pdb=" O ASN H 124 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG H 301 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 156 through 157 removed outlier: 3.928A pdb=" N GLN H 186 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU H 210 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL H 192 " --> pdb=" O GLU H 208 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU H 208 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG H 194 " --> pdb=" O PHE H 206 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE H 206 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER H 196 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER H 204 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 211 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY H 235 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 337 through 340 836 hydrogen bonds defined for protein. 2013 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: 4.91 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3814 1.31 - 1.44: 6064 1.44 - 1.57: 12422 1.57 - 1.70: 0 1.70 - 1.83: 154 Bond restraints: 22454 Sorted by residual: bond pdb=" C VAL E 300 " pdb=" N ASP E 301 " ideal model delta sigma weight residual 1.330 1.220 0.110 1.38e-02 5.25e+03 6.32e+01 bond pdb=" C VAL B 550 " pdb=" N GLY B 551 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CA PRO A 381 " pdb=" C PRO A 381 " ideal model delta sigma weight residual 1.514 1.546 -0.032 5.50e-03 3.31e+04 3.36e+01 bond pdb=" C ARG B 549 " pdb=" N VAL B 550 " ideal model delta sigma weight residual 1.332 1.255 0.077 1.36e-02 5.41e+03 3.19e+01 bond pdb=" C ASP E 301 " pdb=" N HIS E 302 " ideal model delta sigma weight residual 1.333 1.271 0.062 1.50e-02 4.44e+03 1.71e+01 ... (remaining 22449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 22139 1.88 - 3.76: 7191 3.76 - 5.65: 1035 5.65 - 7.53: 123 7.53 - 9.41: 12 Bond angle restraints: 30500 Sorted by residual: angle pdb=" C VAL B 550 " pdb=" N GLY B 551 " pdb=" CA GLY B 551 " ideal model delta sigma weight residual 122.30 114.84 7.46 1.03e+00 9.43e-01 5.24e+01 angle pdb=" CA ASP D 564 " pdb=" CB ASP D 564 " pdb=" CG ASP D 564 " ideal model delta sigma weight residual 112.60 119.59 -6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" CA PHE B 590 " pdb=" CB PHE B 590 " pdb=" CG PHE B 590 " ideal model delta sigma weight residual 113.80 120.62 -6.82 1.00e+00 1.00e+00 4.65e+01 angle pdb=" CA ASP B 174 " pdb=" CB ASP B 174 " pdb=" CG ASP B 174 " ideal model delta sigma weight residual 112.60 118.62 -6.02 1.00e+00 1.00e+00 3.63e+01 angle pdb=" N ASP D 512 " pdb=" CA ASP D 512 " pdb=" C ASP D 512 " ideal model delta sigma weight residual 108.96 99.55 9.41 1.59e+00 3.96e-01 3.50e+01 ... (remaining 30495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11903 17.97 - 35.94: 814 35.94 - 53.91: 153 53.91 - 71.88: 51 71.88 - 89.86: 25 Dihedral angle restraints: 12946 sinusoidal: 5116 harmonic: 7830 Sorted by residual: dihedral pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " pdb=" SG CYS D 559 " pdb=" CB CYS D 559 " ideal model delta sinusoidal sigma weight residual -86.00 -151.03 65.03 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual 93.00 157.36 -64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CB CYS C 557 " pdb=" SG CYS C 557 " pdb=" SG CYS C 559 " pdb=" CB CYS C 559 " ideal model delta sinusoidal sigma weight residual -86.00 -147.38 61.38 1 1.00e+01 1.00e-02 5.00e+01 ... (remaining 12943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2208 0.099 - 0.198: 1024 0.198 - 0.297: 178 0.297 - 0.395: 23 0.395 - 0.494: 6 Chirality restraints: 3439 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.37e+01 ... (remaining 3436 not shown) Planarity restraints: 3923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 199 " -0.158 2.00e-02 2.50e+03 8.23e-02 1.69e+02 pdb=" CG TRP H 199 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP H 199 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TRP H 199 " 0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP H 199 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP H 199 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP H 199 " 0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 199 " -0.113 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 199 " 0.064 2.00e-02 2.50e+03 pdb=" CH2 TRP H 199 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 199 " 0.153 2.00e-02 2.50e+03 7.99e-02 1.60e+02 pdb=" CG TRP A 199 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 199 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP A 199 " -0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP A 199 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP A 199 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 199 " -0.104 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 199 " 0.098 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 199 " -0.045 2.00e-02 2.50e+03 pdb=" CH2 TRP A 199 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 436 " 0.123 2.00e-02 2.50e+03 6.80e-02 1.16e+02 pdb=" CG TRP B 436 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 436 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 436 " -0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP B 436 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP B 436 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP B 436 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 436 " 0.067 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 436 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 436 " 0.085 2.00e-02 2.50e+03 ... (remaining 3920 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 23 2.36 - 2.99: 11861 2.99 - 3.63: 32582 3.63 - 4.26: 56311 4.26 - 4.90: 90232 Nonbonded interactions: 191009 Sorted by model distance: nonbonded pdb=" OD2 ASP A 153 " pdb="ZN ZN A 401 " model vdw 1.724 2.230 nonbonded pdb=" OD1 ASP B 285 " pdb="CA CA B 701 " model vdw 2.158 2.510 nonbonded pdb=" OD1 ASP C 288 " pdb="CA CA C 701 " model vdw 2.262 2.510 nonbonded pdb=" CG ASP A 153 " pdb="ZN ZN A 401 " model vdw 2.267 2.460 nonbonded pdb=" OD1 ASP B 288 " pdb="CA CA B 701 " model vdw 2.269 2.510 ... (remaining 191004 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 31 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 152 or (resid 153 and \ (name N or name CA or name C or name O or name CB )) or resid 154 through 382)) \ selection = (chain 'H' and (resid 31 through 53 or (resid 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 56 or (resid 57 and (name N or nam \ e CA or name C or name O or name CB )) or resid 58 through 65 or (resid 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 74 or re \ sid 79 through 127 or (resid 128 and (name N or name CA or name C or name O or n \ ame CB )) or resid 129 through 242 or (resid 243 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 244 through 310 or (res \ id 324 through 335 and (name N or name CA or name C or name O or name CB )) or r \ esid 336 or (resid 337 through 361 and (name N or name CA or name C or name O or \ name CB )) or resid 366 through 382)) } ncs_group { reference = (chain 'B' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 241 or (resid 242 \ and (name N or name CA or name C or name O or name CB )) or resid 243 through 27 \ 1 or (resid 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 295 or resid 299 through 324 or (resid 325 and (name N or name CA \ or name C or name O or name CB )) or resid 326 through 332 or (resid 333 and (na \ me N or name CA or name C or name O or name CB )) or resid 334 through 407 or (r \ esid 408 and (name N or name CA or name C or name O or name CB )) or resid 409 t \ hrough 533 or (resid 534 and (name N or name CA or name C or name O or name CB ) \ ) or resid 535 through 536 or resid 540 through 548 or (resid 549 and (name N or \ name CA or name C or name O or name CB )) or resid 550 through 560 or (resid 56 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 562 through \ 701)) selection = (chain 'C' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 271 or (resid 272 \ and (name N or name CA or name C or name O or name CB )) or resid 273 through 28 \ 3 or (resid 284 and (name N or name CA or name C or name O or name CB )) or resi \ d 285 through 407 or (resid 408 and (name N or name CA or name C or name O or na \ me CB )) or resid 409 through 476 or (resid 477 and (name N or name CA or name C \ or name O or name CB )) or resid 478 through 548 or (resid 549 and (name N or n \ ame CA or name C or name O or name CB )) or resid 550 through 560 or (resid 561 \ and (name N or name CA or name C or name O or name CB )) or resid 562 through 70 \ 1)) selection = (chain 'D' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 171 or (resid 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 241 or (resid 242 \ and (name N or name CA or name C or name O or name CB )) or resid 243 through 27 \ 1 or (resid 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 283 or (resid 284 and (name N or name CA or name C or name O or na \ me CB )) or resid 285 through 295 or resid 299 through 324 or (resid 325 and (na \ me N or name CA or name C or name O or name CB )) or resid 326 through 332 or (r \ esid 333 and (name N or name CA or name C or name O or name CB )) or resid 334 t \ hrough 407 or (resid 408 and (name N or name CA or name C or name O or name CB ) \ ) or resid 409 through 476 or (resid 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 533 or (resid 534 and (name N or name CA \ or name C or name O or name CB )) or resid 535 through 536 or resid 540 through \ 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or re \ sid 550 through 701)) selection = (chain 'E' and (resid 66 through 241 or (resid 242 and (name N or name CA or nam \ e C or name O or name CB )) or resid 243 through 283 or (resid 284 and (name N o \ r name CA or name C or name O or name CB )) or resid 285 through 295 or resid 29 \ 9 through 324 or (resid 325 and (name N or name CA or name C or name O or name C \ B )) or resid 326 through 332 or (resid 333 and (name N or name CA or name C or \ name O or name CB )) or resid 334 through 476 or (resid 477 and (name N or name \ CA or name C or name O or name CB )) or resid 478 through 533 or (resid 534 and \ (name N or name CA or name C or name O or name CB )) or resid 535 through 536 or \ resid 540 through 701)) } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.620 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.016 0.530 22542 Z= 0.881 Angle : 1.808 11.615 30697 Z= 1.208 Chirality : 0.107 0.494 3439 Planarity : 0.013 0.114 3904 Dihedral : 13.849 89.856 7815 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 1.03 % Allowed : 4.86 % Favored : 94.11 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 2658 helix: -0.98 (0.24), residues: 355 sheet: -0.42 (0.20), residues: 636 loop : -0.56 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 549 TYR 0.113 0.017 TYR A 148 PHE 0.100 0.013 PHE A 206 TRP 0.158 0.023 TRP H 199 HIS 0.016 0.004 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.01329 / 0.82 (22454) covalent geometry : angle 1.78450 / 1.21 (30500) SS BOND : bond 0.02169 / 1.40 ( 31) SS BOND : angle 2.64468 / 1.84 ( 62) hydrogen bonds : bond 0.14798 / 9.27 ( 800) hydrogen bonds : angle 8.20270 / 5.84 ( 2013) metal coordination : bond 0.41742 / 24.26 ( 12) link_BETA1-4 : bond 0.02427 / 1.52 ( 22) link_BETA1-4 : angle 4.97740 / 3.79 ( 66) link_BETA1-6 : bond 0.01734 / 0.86 ( 4) link_BETA1-6 : angle 2.91995 / 1.87 ( 12) link_NAG-ASN : bond 0.01045 / 0.70 ( 19) link_NAG-ASN : angle 4.28934 / 2.90 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 667 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 104 LEU cc_start: 0.8787 (tp) cc_final: 0.8488 (tp) REVERT: E 116 GLU cc_start: 0.7778 (mp0) cc_final: 0.7185 (mp0) REVERT: E 122 PHE cc_start: 0.9276 (m-80) cc_final: 0.9074 (m-80) REVERT: E 124 GLN cc_start: 0.7885 (tt0) cc_final: 0.7627 (tp40) REVERT: E 136 HIS cc_start: 0.7916 (m-70) cc_final: 0.7648 (m-70) REVERT: E 141 ILE cc_start: 0.9042 (mt) cc_final: 0.8837 (mp) REVERT: E 143 ILE cc_start: 0.8254 (mt) cc_final: 0.8034 (mm) REVERT: E 201 ASP cc_start: 0.8670 (p0) cc_final: 0.8456 (m-30) REVERT: E 207 ASP cc_start: 0.7842 (t0) cc_final: 0.7318 (t0) REVERT: E 210 SER cc_start: 0.9123 (t) cc_final: 0.8571 (t) REVERT: E 263 HIS cc_start: 0.7625 (m-70) cc_final: 0.6981 (m-70) REVERT: E 338 LYS cc_start: 0.9149 (mttm) cc_final: 0.8913 (mtpm) REVERT: E 389 LYS cc_start: 0.8835 (mttp) cc_final: 0.8472 (mttm) REVERT: E 409 LYS cc_start: 0.8679 (mttt) cc_final: 0.8431 (mtmt) REVERT: E 423 ASP cc_start: 0.7934 (m-30) cc_final: 0.7526 (m-30) REVERT: E 428 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7103 (mt-10) REVERT: E 443 GLN cc_start: 0.8433 (tt0) cc_final: 0.7690 (tt0) REVERT: E 447 ASN cc_start: 0.8901 (m-40) cc_final: 0.8578 (m110) REVERT: E 453 LYS cc_start: 0.8710 (pttt) cc_final: 0.8407 (ptmt) REVERT: E 514 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7619 (mp0) REVERT: E 518 ARG cc_start: 0.8664 (mtm110) cc_final: 0.8284 (mtm-85) REVERT: E 525 MET cc_start: 0.7900 (mmm) cc_final: 0.7160 (mtp) REVERT: E 538 ILE cc_start: 0.7554 (pt) cc_final: 0.7204 (pt) REVERT: E 567 TRP cc_start: 0.7123 (m-90) cc_final: 0.5805 (m-90) REVERT: E 577 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8805 (mtpp) REVERT: A 60 TYR cc_start: 0.8392 (m-80) cc_final: 0.8168 (m-10) REVERT: A 85 THR cc_start: 0.8209 (m) cc_final: 0.7992 (p) REVERT: A 89 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9173 (pp) REVERT: A 106 MET cc_start: 0.8043 (mpt) cc_final: 0.7752 (mpm) REVERT: A 111 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8015 (tm-30) REVERT: A 132 LEU cc_start: 0.8752 (tp) cc_final: 0.8003 (mt) REVERT: A 140 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7476 (mtm-85) REVERT: A 168 LEU cc_start: 0.9089 (tp) cc_final: 0.8879 (tm) REVERT: A 173 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8412 (mm-30) REVERT: A 374 ASN cc_start: 0.9112 (t0) cc_final: 0.8513 (p0) REVERT: B 154 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 215 GLN cc_start: 0.8242 (pt0) cc_final: 0.7812 (pp30) REVERT: B 235 PHE cc_start: 0.8929 (m-80) cc_final: 0.8267 (m-80) REVERT: B 245 PHE cc_start: 0.9073 (m-80) cc_final: 0.8769 (m-10) REVERT: B 266 LEU cc_start: 0.9212 (tp) cc_final: 0.8884 (tt) REVERT: B 502 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7090 (mt-10) REVERT: B 521 MET cc_start: 0.8568 (mtp) cc_final: 0.8142 (mtp) REVERT: C 131 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: C 149 TYR cc_start: 0.8426 (m-10) cc_final: 0.8153 (m-80) REVERT: C 187 TYR cc_start: 0.8586 (m-80) cc_final: 0.8255 (m-80) REVERT: C 195 ASP cc_start: 0.7264 (p0) cc_final: 0.6858 (p0) REVERT: C 197 SER cc_start: 0.9289 (t) cc_final: 0.8975 (p) REVERT: C 212 MET cc_start: 0.8830 (mmm) cc_final: 0.8332 (mmt) REVERT: C 245 PHE cc_start: 0.8802 (m-80) cc_final: 0.8102 (m-10) REVERT: C 263 HIS cc_start: 0.8025 (m-70) cc_final: 0.7487 (m170) REVERT: C 331 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 525 MET cc_start: 0.7931 (mmm) cc_final: 0.7280 (mmm) REVERT: C 543 ILE cc_start: 0.8857 (mt) cc_final: 0.8649 (tt) REVERT: C 584 ASN cc_start: 0.8602 (t0) cc_final: 0.7973 (t0) REVERT: D 212 MET cc_start: 0.9409 (mmm) cc_final: 0.9091 (mmm) REVERT: D 238 ILE cc_start: 0.8927 (mt) cc_final: 0.8653 (mm) REVERT: D 251 GLU cc_start: 0.7559 (tt0) cc_final: 0.7316 (tt0) REVERT: D 253 LEU cc_start: 0.9194 (tp) cc_final: 0.8953 (tt) REVERT: D 315 MET cc_start: 0.8837 (mmm) cc_final: 0.8580 (mmt) REVERT: D 396 LYS cc_start: 0.8675 (mttt) cc_final: 0.8470 (mtmp) REVERT: D 517 VAL cc_start: 0.9243 (t) cc_final: 0.9025 (m) REVERT: H 41 VAL cc_start: 0.5990 (t) cc_final: 0.5691 (m) REVERT: H 74 ARG cc_start: 0.8853 (mtt180) cc_final: 0.8480 (tpp-160) REVERT: H 128 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8044 (mmm160) REVERT: H 135 TYR cc_start: 0.8148 (p90) cc_final: 0.7645 (p90) REVERT: H 149 MET cc_start: 0.8232 (mmm) cc_final: 0.7959 (mtm) REVERT: H 199 TRP cc_start: 0.7863 (t-100) cc_final: 0.7603 (t60) REVERT: H 205 TYR cc_start: 0.8883 (m-80) cc_final: 0.8519 (m-80) REVERT: H 212 LYS cc_start: 0.8716 (pttt) cc_final: 0.8285 (mtmm) REVERT: H 307 LEU cc_start: 0.8866 (mt) cc_final: 0.8620 (pt) outliers start: 24 outliers final: 5 residues processed: 685 average time/residue: 0.4959 time to fit residues: 393.1795 Evaluate side-chains 424 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 417 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain H residue 122 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 72 ASN E 341 GLN E 381 GLN E 386 HIS E 474 ASN E 513 GLN E 573 HIS E 584 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN B 341 GLN B 513 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN C 386 HIS C 455 GLN C 505 GLN C 513 GLN C 558 ASN D 72 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 307 GLN D 341 GLN D 455 GLN D 503 ASN D 513 GLN ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108221 restraints weight = 41579.320| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.35 r_work: 0.3363 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22542 Z= 0.186 Angle : 0.766 9.168 30697 Z= 0.403 Chirality : 0.048 0.161 3439 Planarity : 0.005 0.055 3904 Dihedral : 7.002 60.614 2921 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.10 % Allowed : 15.53 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2658 helix: 0.44 (0.26), residues: 359 sheet: -0.43 (0.19), residues: 706 loop : -0.10 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 578 TYR 0.027 0.002 TYR A 131 PHE 0.031 0.002 PHE A 121 TRP 0.023 0.002 TRP E 361 HIS 0.010 0.002 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (22454) covalent geometry : angle 0.74962 / 0.40 (30500) SS BOND : bond 0.00403 / 0.25 ( 31) SS BOND : angle 1.17064 / 0.92 ( 62) hydrogen bonds : bond 0.05039 / 3.26 ( 800) hydrogen bonds : angle 6.52722 / 4.68 ( 2013) metal coordination : bond 0.01600 / 0.94 ( 12) link_BETA1-4 : bond 0.00603 / 0.38 ( 22) link_BETA1-4 : angle 2.17043 / 1.53 ( 66) link_BETA1-6 : bond 0.00393 / 0.20 ( 4) link_BETA1-6 : angle 1.28605 / 0.85 ( 12) link_NAG-ASN : bond 0.00397 / 0.23 ( 19) link_NAG-ASN : angle 2.78748 / 1.83 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 437 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: E 129 TRP cc_start: 0.7520 (p-90) cc_final: 0.7168 (p-90) REVERT: E 143 ILE cc_start: 0.8219 (mt) cc_final: 0.7820 (mm) REVERT: E 201 ASP cc_start: 0.8577 (p0) cc_final: 0.8306 (t0) REVERT: E 207 ASP cc_start: 0.7454 (t0) cc_final: 0.7208 (t0) REVERT: E 215 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7603 (tm-30) REVERT: E 256 MET cc_start: 0.8469 (ttp) cc_final: 0.8143 (ttt) REVERT: E 263 HIS cc_start: 0.7756 (m-70) cc_final: 0.7237 (t70) REVERT: E 308 CYS cc_start: 0.8969 (t) cc_final: 0.8738 (p) REVERT: E 338 LYS cc_start: 0.9486 (mttm) cc_final: 0.9262 (mttp) REVERT: E 340 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7883 (mmmt) REVERT: E 399 GLN cc_start: 0.6443 (pm20) cc_final: 0.6043 (pm20) REVERT: E 423 ASP cc_start: 0.8375 (m-30) cc_final: 0.7844 (m-30) REVERT: E 447 ASN cc_start: 0.9132 (m-40) cc_final: 0.8779 (m-40) REVERT: E 453 LYS cc_start: 0.8819 (pttt) cc_final: 0.8422 (ptmm) REVERT: E 471 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7646 (tm) REVERT: E 514 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7281 (mp0) REVERT: E 525 MET cc_start: 0.8580 (mmm) cc_final: 0.8001 (mtp) REVERT: E 574 GLN cc_start: 0.8867 (pt0) cc_final: 0.8405 (pm20) REVERT: A 97 ARG cc_start: 0.7171 (tpm170) cc_final: 0.6383 (tpm170) REVERT: A 99 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8139 (ttpp) REVERT: A 111 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8285 (tm-30) REVERT: A 118 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.5799 (mtpt) REVERT: A 169 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 173 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 199 TRP cc_start: 0.7130 (m100) cc_final: 0.6737 (m-10) REVERT: A 255 ASP cc_start: 0.7848 (p0) cc_final: 0.7271 (p0) REVERT: A 374 ASN cc_start: 0.9014 (t0) cc_final: 0.8305 (p0) REVERT: A 380 LEU cc_start: 0.9176 (tp) cc_final: 0.8713 (mt) REVERT: B 149 TYR cc_start: 0.7551 (m-10) cc_final: 0.7341 (m-10) REVERT: B 154 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8476 (mt-10) REVERT: B 214 TYR cc_start: 0.8601 (m-10) cc_final: 0.8277 (m-80) REVERT: B 215 GLN cc_start: 0.8639 (pt0) cc_final: 0.7957 (pp30) REVERT: B 235 PHE cc_start: 0.9007 (m-80) cc_final: 0.8173 (m-80) REVERT: B 251 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8500 (mm-30) REVERT: B 351 THR cc_start: 0.8751 (p) cc_final: 0.8532 (p) REVERT: B 450 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8901 (tptt) REVERT: B 503 ASN cc_start: 0.8944 (m-40) cc_final: 0.8554 (m110) REVERT: B 521 MET cc_start: 0.8999 (mtp) cc_final: 0.8779 (mtm) REVERT: C 172 ARG cc_start: 0.9013 (ppt-90) cc_final: 0.8607 (ppt-90) REVERT: C 195 ASP cc_start: 0.7714 (p0) cc_final: 0.7193 (p0) REVERT: C 197 SER cc_start: 0.9466 (t) cc_final: 0.9258 (p) REVERT: C 212 MET cc_start: 0.9110 (mmm) cc_final: 0.8223 (mmt) REVERT: C 244 ASP cc_start: 0.8210 (p0) cc_final: 0.7982 (p0) REVERT: C 245 PHE cc_start: 0.8712 (m-80) cc_final: 0.8331 (m-10) REVERT: C 280 ILE cc_start: 0.8523 (pt) cc_final: 0.8279 (pp) REVERT: C 356 ASP cc_start: 0.8206 (m-30) cc_final: 0.7690 (m-30) REVERT: C 521 MET cc_start: 0.8654 (mtm) cc_final: 0.8144 (ttp) REVERT: C 525 MET cc_start: 0.8563 (mmm) cc_final: 0.8129 (mtp) REVERT: C 531 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8927 (mtpp) REVERT: D 121 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8631 (tp) REVERT: D 189 HIS cc_start: 0.7233 (p-80) cc_final: 0.6700 (p-80) REVERT: D 212 MET cc_start: 0.9540 (mmm) cc_final: 0.9269 (mmm) REVERT: D 215 GLN cc_start: 0.8975 (tt0) cc_final: 0.8505 (tm-30) REVERT: D 249 ASP cc_start: 0.8443 (m-30) cc_final: 0.7963 (m-30) REVERT: D 272 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: D 315 MET cc_start: 0.9182 (mmm) cc_final: 0.8920 (mmt) REVERT: D 424 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 463 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: D 492 GLU cc_start: 0.8540 (pt0) cc_final: 0.8293 (pm20) REVERT: D 498 GLU cc_start: 0.8201 (pt0) cc_final: 0.7949 (pt0) REVERT: H 41 VAL cc_start: 0.6174 (t) cc_final: 0.5889 (m) REVERT: H 60 TYR cc_start: 0.8004 (m-80) cc_final: 0.7501 (m-80) REVERT: H 65 ASN cc_start: 0.8432 (t0) cc_final: 0.8232 (t0) REVERT: H 187 TYR cc_start: 0.9118 (m-80) cc_final: 0.8368 (m-10) REVERT: H 238 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7183 (mppt) REVERT: H 307 LEU cc_start: 0.8889 (mt) cc_final: 0.8678 (pp) outliers start: 72 outliers final: 17 residues processed: 472 average time/residue: 0.5134 time to fit residues: 281.3126 Evaluate side-chains 390 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 363 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 580 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 238 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 455 GLN E 474 ASN E 573 HIS E 584 ASN A 37 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 307 GLN D 392 HIS ** D 399 GLN ** 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 = 0.4091 r_free = 0.4091 target = 0.150663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106754 restraints weight = 41173.532| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.35 r_work: 0.3320 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22542 Z= 0.185 Angle : 0.700 11.374 30697 Z= 0.363 Chirality : 0.045 0.161 3439 Planarity : 0.004 0.063 3904 Dihedral : 6.004 52.438 2911 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.53 % Allowed : 16.95 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2658 helix: 0.60 (0.26), residues: 359 sheet: -0.58 (0.18), residues: 758 loop : -0.05 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 578 TYR 0.040 0.002 TYR A 178 PHE 0.028 0.002 PHE A 110 TRP 0.035 0.002 TRP H 199 HIS 0.012 0.001 HIS D 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (22454) covalent geometry : angle 0.68838 / 0.36 (30500) SS BOND : bond 0.00397 / 0.26 ( 31) SS BOND : angle 1.08305 / 0.72 ( 62) hydrogen bonds : bond 0.04306 / 2.79 ( 800) hydrogen bonds : angle 6.08849 / 4.34 ( 2013) metal coordination : bond 0.00567 / 0.47 ( 12) link_BETA1-4 : bond 0.00414 / 0.27 ( 22) link_BETA1-4 : angle 1.70963 / 1.23 ( 66) link_BETA1-6 : bond 0.00382 / 0.20 ( 4) link_BETA1-6 : angle 1.27855 / 0.88 ( 12) link_NAG-ASN : bond 0.00243 / 0.16 ( 19) link_NAG-ASN : angle 2.27094 / 1.51 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 399 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: E 129 TRP cc_start: 0.7760 (p-90) cc_final: 0.7201 (p-90) REVERT: E 190 ASN cc_start: 0.6954 (m-40) cc_final: 0.6581 (m-40) REVERT: E 201 ASP cc_start: 0.8610 (p0) cc_final: 0.8315 (t0) REVERT: E 212 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6214 (mmm) REVERT: E 215 GLN cc_start: 0.8012 (tt0) cc_final: 0.7554 (tm-30) REVERT: E 242 ARG cc_start: 0.8491 (mmt90) cc_final: 0.8070 (mmt90) REVERT: E 256 MET cc_start: 0.8686 (ttp) cc_final: 0.8428 (ttt) REVERT: E 263 HIS cc_start: 0.7716 (m-70) cc_final: 0.7349 (t70) REVERT: E 338 LYS cc_start: 0.9487 (mttm) cc_final: 0.9280 (mtpp) REVERT: E 399 GLN cc_start: 0.6678 (pm20) cc_final: 0.6293 (pm20) REVERT: E 423 ASP cc_start: 0.8254 (m-30) cc_final: 0.7956 (m-30) REVERT: E 438 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7672 (m) REVERT: E 443 GLN cc_start: 0.8179 (tt0) cc_final: 0.7476 (pt0) REVERT: E 447 ASN cc_start: 0.9122 (m-40) cc_final: 0.8740 (p0) REVERT: E 453 LYS cc_start: 0.8824 (pttt) cc_final: 0.8515 (ptmm) REVERT: E 514 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7336 (mp0) REVERT: E 525 MET cc_start: 0.8581 (mmm) cc_final: 0.8059 (mtp) REVERT: E 574 GLN cc_start: 0.8783 (pt0) cc_final: 0.8320 (pm20) REVERT: E 586 ASP cc_start: 0.7567 (p0) cc_final: 0.7181 (p0) REVERT: A 63 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7145 (mtt180) REVERT: A 67 VAL cc_start: 0.6739 (OUTLIER) cc_final: 0.6344 (p) REVERT: A 69 ASP cc_start: 0.6821 (t70) cc_final: 0.6326 (t70) REVERT: A 97 ARG cc_start: 0.7541 (tpm170) cc_final: 0.6951 (tpm170) REVERT: A 106 MET cc_start: 0.7748 (mpt) cc_final: 0.7347 (mmt) REVERT: A 111 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8168 (tm-30) REVERT: A 140 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6355 (mpp80) REVERT: A 169 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 173 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8238 (mm-30) REVERT: A 199 TRP cc_start: 0.7320 (m100) cc_final: 0.6842 (m-10) REVERT: A 255 ASP cc_start: 0.7466 (p0) cc_final: 0.7207 (p0) REVERT: A 374 ASN cc_start: 0.8955 (t0) cc_final: 0.8114 (p0) REVERT: A 380 LEU cc_start: 0.9143 (tp) cc_final: 0.8678 (mt) REVERT: B 132 VAL cc_start: 0.9088 (t) cc_final: 0.8794 (m) REVERT: B 154 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 214 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: B 215 GLN cc_start: 0.8681 (pt0) cc_final: 0.7996 (pp30) REVERT: B 235 PHE cc_start: 0.9040 (m-80) cc_final: 0.8197 (m-80) REVERT: B 251 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8561 (mm-30) REVERT: B 428 GLU cc_start: 0.8745 (mp0) cc_final: 0.8534 (mp0) REVERT: B 453 LYS cc_start: 0.8511 (ptmm) cc_final: 0.8239 (ptmm) REVERT: B 503 ASN cc_start: 0.8899 (m-40) cc_final: 0.8612 (m110) REVERT: C 172 ARG cc_start: 0.9076 (ppt-90) cc_final: 0.8252 (ptt-90) REVERT: C 195 ASP cc_start: 0.7786 (p0) cc_final: 0.7202 (p0) REVERT: C 197 SER cc_start: 0.9503 (t) cc_final: 0.9293 (p) REVERT: C 212 MET cc_start: 0.9075 (mmm) cc_final: 0.8251 (mmt) REVERT: C 245 PHE cc_start: 0.8780 (m-80) cc_final: 0.8448 (m-10) REVERT: C 356 ASP cc_start: 0.8442 (m-30) cc_final: 0.7903 (m-30) REVERT: C 463 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8238 (tp30) REVERT: C 584 ASN cc_start: 0.8647 (t0) cc_final: 0.7741 (t0) REVERT: D 109 ASP cc_start: 0.8734 (t0) cc_final: 0.8377 (t0) REVERT: D 212 MET cc_start: 0.9548 (mmm) cc_final: 0.9229 (mmm) REVERT: D 215 GLN cc_start: 0.9059 (tt0) cc_final: 0.8652 (tm-30) REVERT: D 272 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8334 (mp0) REVERT: D 340 LYS cc_start: 0.9030 (mptt) cc_final: 0.7740 (mptt) REVERT: D 398 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: D 498 GLU cc_start: 0.8094 (pt0) cc_final: 0.7871 (pt0) REVERT: H 41 VAL cc_start: 0.6242 (t) cc_final: 0.5974 (m) REVERT: H 60 TYR cc_start: 0.7952 (m-80) cc_final: 0.7557 (m-80) REVERT: H 199 TRP cc_start: 0.8060 (t-100) cc_final: 0.7523 (t60) REVERT: H 238 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7023 (mppt) REVERT: H 249 PHE cc_start: 0.8071 (m-80) cc_final: 0.7747 (m-10) outliers start: 82 outliers final: 31 residues processed: 445 average time/residue: 0.5144 time to fit residues: 265.8475 Evaluate side-chains 394 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 353 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 238 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 57 optimal weight: 50.0000 chunk 81 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 474 ASN E 573 HIS E 584 ASN A 37 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109210 restraints weight = 41282.579| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.33 r_work: 0.3378 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22542 Z= 0.141 Angle : 0.660 10.240 30697 Z= 0.339 Chirality : 0.044 0.171 3439 Planarity : 0.004 0.051 3904 Dihedral : 5.536 35.744 2910 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.84 % Allowed : 19.27 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2658 helix: 0.70 (0.27), residues: 359 sheet: -0.52 (0.18), residues: 755 loop : -0.01 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 504 TYR 0.038 0.002 TYR H 135 PHE 0.031 0.002 PHE A 121 TRP 0.017 0.001 TRP D 567 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (22454) covalent geometry : angle 0.65123 / 0.34 (30500) SS BOND : bond 0.00444 / 0.30 ( 31) SS BOND : angle 0.99341 / 0.65 ( 62) hydrogen bonds : bond 0.03914 / 2.51 ( 800) hydrogen bonds : angle 5.90916 / 4.19 ( 2013) metal coordination : bond 0.00347 / 0.31 ( 12) link_BETA1-4 : bond 0.00355 / 0.24 ( 22) link_BETA1-4 : angle 1.51782 / 1.10 ( 66) link_BETA1-6 : bond 0.00419 / 0.21 ( 4) link_BETA1-6 : angle 1.19162 / 0.82 ( 12) link_NAG-ASN : bond 0.00168 / 0.11 ( 19) link_NAG-ASN : angle 1.94586 / 1.30 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 388 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7603 (t0) cc_final: 0.6460 (m-30) REVERT: E 129 TRP cc_start: 0.7689 (p-90) cc_final: 0.7121 (p-90) REVERT: E 190 ASN cc_start: 0.6943 (m-40) cc_final: 0.6573 (m-40) REVERT: E 201 ASP cc_start: 0.8624 (p0) cc_final: 0.8287 (t0) REVERT: E 215 GLN cc_start: 0.7972 (tt0) cc_final: 0.7473 (tm-30) REVERT: E 256 MET cc_start: 0.8765 (ttp) cc_final: 0.8482 (ttt) REVERT: E 263 HIS cc_start: 0.7807 (m-70) cc_final: 0.7324 (t70) REVERT: E 338 LYS cc_start: 0.9482 (mttm) cc_final: 0.9279 (mtpp) REVERT: E 340 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7989 (mmmt) REVERT: E 370 ASN cc_start: 0.8634 (t0) cc_final: 0.8319 (t0) REVERT: E 399 GLN cc_start: 0.6773 (pm20) cc_final: 0.6125 (pm20) REVERT: E 443 GLN cc_start: 0.8107 (tt0) cc_final: 0.7610 (pt0) REVERT: E 447 ASN cc_start: 0.9091 (m-40) cc_final: 0.8768 (p0) REVERT: E 453 LYS cc_start: 0.8927 (pttt) cc_final: 0.8508 (ptmm) REVERT: E 471 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7822 (tm) REVERT: E 525 MET cc_start: 0.8517 (mmm) cc_final: 0.7977 (mtp) REVERT: E 571 ILE cc_start: 0.8413 (tp) cc_final: 0.8168 (tt) REVERT: E 579 ARG cc_start: 0.7530 (mmm160) cc_final: 0.6983 (ttt90) REVERT: E 586 ASP cc_start: 0.7643 (p0) cc_final: 0.7322 (p0) REVERT: A 63 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.6928 (mtt90) REVERT: A 65 ASN cc_start: 0.8782 (t0) cc_final: 0.5835 (m110) REVERT: A 72 GLU cc_start: 0.6478 (tp30) cc_final: 0.6225 (mm-30) REVERT: A 97 ARG cc_start: 0.7699 (tpm170) cc_final: 0.7317 (tpp-160) REVERT: A 106 MET cc_start: 0.7586 (mpt) cc_final: 0.7289 (mmt) REVERT: A 111 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8138 (tm-30) REVERT: A 140 ARG cc_start: 0.7292 (mtt180) cc_final: 0.6205 (mpp80) REVERT: A 169 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 173 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 181 GLU cc_start: 0.9588 (pp20) cc_final: 0.9348 (pp20) REVERT: A 199 TRP cc_start: 0.7440 (m100) cc_final: 0.7141 (m-10) REVERT: A 301 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7562 (mmm160) REVERT: A 374 ASN cc_start: 0.8937 (t0) cc_final: 0.8275 (p0) REVERT: A 380 LEU cc_start: 0.9074 (tp) cc_final: 0.8600 (mt) REVERT: B 132 VAL cc_start: 0.9007 (t) cc_final: 0.8668 (m) REVERT: B 154 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 198 LEU cc_start: 0.9164 (tp) cc_final: 0.8945 (tp) REVERT: B 214 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: B 215 GLN cc_start: 0.8611 (pt0) cc_final: 0.7884 (pp30) REVERT: B 235 PHE cc_start: 0.8925 (m-80) cc_final: 0.8660 (m-80) REVERT: B 251 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8499 (mt-10) REVERT: B 266 LEU cc_start: 0.9067 (tp) cc_final: 0.8669 (mt) REVERT: B 428 GLU cc_start: 0.8764 (mp0) cc_final: 0.7486 (mp0) REVERT: B 453 LYS cc_start: 0.8494 (ptmm) cc_final: 0.7555 (tttm) REVERT: B 503 ASN cc_start: 0.8897 (m-40) cc_final: 0.8616 (m110) REVERT: C 195 ASP cc_start: 0.7879 (p0) cc_final: 0.7330 (p0) REVERT: C 197 SER cc_start: 0.9523 (t) cc_final: 0.9303 (p) REVERT: C 212 MET cc_start: 0.9022 (mmm) cc_final: 0.8122 (mmt) REVERT: C 245 PHE cc_start: 0.8774 (m-80) cc_final: 0.8466 (m-10) REVERT: C 248 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9215 (tp) REVERT: C 356 ASP cc_start: 0.8497 (m-30) cc_final: 0.7948 (m-30) REVERT: C 463 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8341 (tp30) REVERT: C 525 MET cc_start: 0.9066 (mtp) cc_final: 0.8648 (mtp) REVERT: C 531 LYS cc_start: 0.9300 (ptpp) cc_final: 0.9031 (mtpp) REVERT: C 584 ASN cc_start: 0.8691 (t0) cc_final: 0.7742 (t0) REVERT: D 109 ASP cc_start: 0.8719 (t0) cc_final: 0.8271 (t70) REVERT: D 212 MET cc_start: 0.9512 (mmm) cc_final: 0.9190 (mmm) REVERT: D 214 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.6841 (m-10) REVERT: D 215 GLN cc_start: 0.9064 (tt0) cc_final: 0.8649 (tm-30) REVERT: D 272 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: D 307 GLN cc_start: 0.7588 (tt0) cc_final: 0.7383 (tt0) REVERT: D 340 LYS cc_start: 0.9025 (mptt) cc_final: 0.8021 (mptt) REVERT: D 398 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: D 463 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: D 498 GLU cc_start: 0.8013 (pt0) cc_final: 0.7780 (pt0) REVERT: D 524 SER cc_start: 0.8334 (t) cc_final: 0.8093 (p) REVERT: H 41 VAL cc_start: 0.6291 (t) cc_final: 0.6004 (m) REVERT: H 51 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8557 (p0) REVERT: H 60 TYR cc_start: 0.7848 (m-80) cc_final: 0.7513 (m-80) REVERT: H 69 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6681 (t70) REVERT: H 199 TRP cc_start: 0.7979 (t-100) cc_final: 0.7446 (t60) REVERT: H 243 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7953 (ttm-80) REVERT: H 247 GLU cc_start: 0.5239 (mm-30) cc_final: 0.5022 (mm-30) outliers start: 66 outliers final: 24 residues processed: 430 average time/residue: 0.5099 time to fit residues: 253.6696 Evaluate side-chains 388 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 353 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 309 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 185 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 158 optimal weight: 0.0060 chunk 47 optimal weight: 0.0470 chunk 150 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 123 GLN E 474 ASN E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.150532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106799 restraints weight = 40706.267| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.35 r_work: 0.3345 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22542 Z= 0.189 Angle : 0.654 8.945 30697 Z= 0.336 Chirality : 0.044 0.206 3439 Planarity : 0.004 0.043 3904 Dihedral : 5.369 36.475 2910 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.48 % Allowed : 19.23 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2658 helix: 0.73 (0.26), residues: 365 sheet: -0.60 (0.18), residues: 763 loop : 0.01 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 504 TYR 0.024 0.002 TYR H 187 PHE 0.030 0.002 PHE A 121 TRP 0.016 0.001 TRP D 567 HIS 0.014 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (22454) covalent geometry : angle 0.64509 / 0.33 (30500) SS BOND : bond 0.00488 / 0.34 ( 31) SS BOND : angle 0.97973 / 0.64 ( 62) hydrogen bonds : bond 0.03776 / 2.43 ( 800) hydrogen bonds : angle 5.82016 / 4.12 ( 2013) metal coordination : bond 0.00465 / 0.42 ( 12) link_BETA1-4 : bond 0.00312 / 0.20 ( 22) link_BETA1-4 : angle 1.51550 / 1.09 ( 66) link_BETA1-6 : bond 0.00292 / 0.15 ( 4) link_BETA1-6 : angle 1.35653 / 0.94 ( 12) link_NAG-ASN : bond 0.00194 / 0.13 ( 19) link_NAG-ASN : angle 1.87046 / 1.26 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 369 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.6254 (m-30) REVERT: E 120 ILE cc_start: 0.8649 (mt) cc_final: 0.8403 (mm) REVERT: E 123 GLN cc_start: 0.8263 (mm110) cc_final: 0.7455 (mp-120) REVERT: E 129 TRP cc_start: 0.7856 (p-90) cc_final: 0.7358 (p-90) REVERT: E 201 ASP cc_start: 0.8628 (p0) cc_final: 0.8272 (t0) REVERT: E 210 SER cc_start: 0.8542 (t) cc_final: 0.8176 (t) REVERT: E 215 GLN cc_start: 0.8039 (tt0) cc_final: 0.7453 (tm-30) REVERT: E 256 MET cc_start: 0.8927 (ttp) cc_final: 0.8676 (ttt) REVERT: E 263 HIS cc_start: 0.7805 (m-70) cc_final: 0.7448 (t70) REVERT: E 293 ASP cc_start: 0.8731 (t0) cc_final: 0.8414 (p0) REVERT: E 338 LYS cc_start: 0.9471 (mttm) cc_final: 0.9009 (mmtt) REVERT: E 370 ASN cc_start: 0.8661 (t0) cc_final: 0.8266 (t0) REVERT: E 398 GLU cc_start: 0.8047 (pm20) cc_final: 0.7840 (pm20) REVERT: E 438 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7566 (m) REVERT: E 453 LYS cc_start: 0.8856 (pttt) cc_final: 0.8516 (ptmm) REVERT: E 471 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7797 (tm) REVERT: E 514 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7888 (tm-30) REVERT: E 525 MET cc_start: 0.8533 (mmm) cc_final: 0.7967 (mtp) REVERT: E 579 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7070 (ttt90) REVERT: E 586 ASP cc_start: 0.7600 (p0) cc_final: 0.7230 (p0) REVERT: A 63 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.6923 (mtt180) REVERT: A 65 ASN cc_start: 0.8841 (t0) cc_final: 0.5943 (m110) REVERT: A 72 GLU cc_start: 0.6503 (tp30) cc_final: 0.6197 (mm-30) REVERT: A 97 ARG cc_start: 0.7771 (tpm170) cc_final: 0.7372 (tpp-160) REVERT: A 106 MET cc_start: 0.7562 (mpt) cc_final: 0.7352 (mmt) REVERT: A 111 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8163 (tm-30) REVERT: A 123 MET cc_start: 0.8471 (tpt) cc_final: 0.8193 (tmm) REVERT: A 124 ASN cc_start: 0.7403 (p0) cc_final: 0.6981 (p0) REVERT: A 169 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7827 (mm-30) REVERT: A 173 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 374 ASN cc_start: 0.8958 (t0) cc_final: 0.8307 (p0) REVERT: A 380 LEU cc_start: 0.9016 (tp) cc_final: 0.8560 (mt) REVERT: B 83 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 132 VAL cc_start: 0.9078 (t) cc_final: 0.8736 (m) REVERT: B 149 TYR cc_start: 0.7722 (m-10) cc_final: 0.7504 (m-80) REVERT: B 154 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8409 (mt-10) REVERT: B 198 LEU cc_start: 0.9162 (tp) cc_final: 0.8936 (tp) REVERT: B 214 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: B 215 GLN cc_start: 0.8631 (pt0) cc_final: 0.7979 (pp30) REVERT: B 235 PHE cc_start: 0.8928 (m-80) cc_final: 0.8680 (m-80) REVERT: B 251 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: B 428 GLU cc_start: 0.8763 (mp0) cc_final: 0.8490 (mp0) REVERT: B 453 LYS cc_start: 0.8456 (ptmm) cc_final: 0.8196 (ptmm) REVERT: B 484 LEU cc_start: 0.8783 (mt) cc_final: 0.8304 (mp) REVERT: B 503 ASN cc_start: 0.8973 (m-40) cc_final: 0.8758 (m110) REVERT: C 157 ILE cc_start: 0.8885 (mt) cc_final: 0.8681 (mt) REVERT: C 195 ASP cc_start: 0.8047 (p0) cc_final: 0.7464 (p0) REVERT: C 197 SER cc_start: 0.9504 (t) cc_final: 0.9298 (p) REVERT: C 212 MET cc_start: 0.9013 (mmm) cc_final: 0.7994 (mmt) REVERT: C 244 ASP cc_start: 0.8487 (p0) cc_final: 0.8044 (p0) REVERT: C 245 PHE cc_start: 0.8714 (m-80) cc_final: 0.8471 (m-10) REVERT: C 356 ASP cc_start: 0.8431 (m-30) cc_final: 0.7940 (m-30) REVERT: C 463 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: C 518 ARG cc_start: 0.9137 (mtm110) cc_final: 0.8616 (mtm180) REVERT: C 578 ARG cc_start: 0.8308 (ptp-110) cc_final: 0.8018 (ptp-110) REVERT: C 584 ASN cc_start: 0.8759 (t0) cc_final: 0.7850 (t0) REVERT: D 109 ASP cc_start: 0.8812 (t0) cc_final: 0.8394 (t70) REVERT: D 212 MET cc_start: 0.9469 (mmm) cc_final: 0.9202 (mmm) REVERT: D 214 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6876 (m-10) REVERT: D 215 GLN cc_start: 0.9110 (tt0) cc_final: 0.8720 (tm-30) REVERT: D 272 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: D 299 GLU cc_start: 0.8445 (mp0) cc_final: 0.7750 (pp20) REVERT: D 340 LYS cc_start: 0.9008 (mptt) cc_final: 0.8069 (mptt) REVERT: D 398 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: D 463 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: H 41 VAL cc_start: 0.6319 (t) cc_final: 0.6051 (m) REVERT: H 60 TYR cc_start: 0.7774 (m-80) cc_final: 0.7462 (m-80) REVERT: H 69 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6642 (t70) REVERT: H 111 GLU cc_start: 0.7868 (pp20) cc_final: 0.7040 (pm20) REVERT: H 169 GLU cc_start: 0.9474 (tt0) cc_final: 0.9057 (tp30) REVERT: H 199 TRP cc_start: 0.8057 (t-100) cc_final: 0.7634 (t60) REVERT: H 243 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7903 (ttm-80) REVERT: H 244 THR cc_start: 0.7438 (OUTLIER) cc_final: 0.7124 (p) outliers start: 81 outliers final: 33 residues processed: 423 average time/residue: 0.4704 time to fit residues: 231.9371 Evaluate side-chains 397 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 214 TYR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 244 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 14 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 474 ASN E 584 ASN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN D 307 GLN D 513 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.148992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.104940 restraints weight = 41005.971| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.37 r_work: 0.3313 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22542 Z= 0.252 Angle : 0.693 12.841 30697 Z= 0.355 Chirality : 0.045 0.276 3439 Planarity : 0.004 0.053 3904 Dihedral : 5.407 37.104 2910 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.44 % Allowed : 19.78 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2658 helix: 0.34 (0.26), residues: 383 sheet: -0.59 (0.19), residues: 752 loop : -0.08 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 578 TYR 0.031 0.002 TYR A 178 PHE 0.028 0.002 PHE A 121 TRP 0.036 0.002 TRP A 199 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (22454) covalent geometry : angle 0.68481 / 0.35 (30500) SS BOND : bond 0.00538 / 0.37 ( 31) SS BOND : angle 0.99855 / 0.66 ( 62) hydrogen bonds : bond 0.03865 / 2.47 ( 800) hydrogen bonds : angle 5.91379 / 4.16 ( 2013) metal coordination : bond 0.00607 / 0.54 ( 12) link_BETA1-4 : bond 0.00303 / 0.19 ( 22) link_BETA1-4 : angle 1.53284 / 1.10 ( 66) link_BETA1-6 : bond 0.00202 / 0.11 ( 4) link_BETA1-6 : angle 1.47165 / 1.03 ( 12) link_NAG-ASN : bond 0.00298 / 0.20 ( 19) link_NAG-ASN : angle 1.85283 / 1.24 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 354 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: E 123 GLN cc_start: 0.8230 (mm110) cc_final: 0.7493 (mp10) REVERT: E 129 TRP cc_start: 0.7972 (p-90) cc_final: 0.7476 (p-90) REVERT: E 210 SER cc_start: 0.8652 (t) cc_final: 0.8347 (t) REVERT: E 215 GLN cc_start: 0.8090 (tt0) cc_final: 0.7465 (tm-30) REVERT: E 263 HIS cc_start: 0.7839 (m-70) cc_final: 0.7450 (t70) REVERT: E 338 LYS cc_start: 0.9509 (mttm) cc_final: 0.9075 (mmtt) REVERT: E 370 ASN cc_start: 0.8686 (t0) cc_final: 0.8366 (t0) REVERT: E 398 GLU cc_start: 0.8028 (pm20) cc_final: 0.7783 (pm20) REVERT: E 438 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7659 (m) REVERT: E 453 LYS cc_start: 0.8889 (pttt) cc_final: 0.8564 (ptmm) REVERT: E 471 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7877 (tm) REVERT: E 514 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8118 (mm-30) REVERT: E 525 MET cc_start: 0.8497 (mmm) cc_final: 0.7998 (mtp) REVERT: E 586 ASP cc_start: 0.8000 (p0) cc_final: 0.7644 (p0) REVERT: A 63 ARG cc_start: 0.7579 (mtp-110) cc_final: 0.6788 (mtt180) REVERT: A 72 GLU cc_start: 0.6494 (tp30) cc_final: 0.6246 (mm-30) REVERT: A 97 ARG cc_start: 0.7481 (tpm170) cc_final: 0.6969 (tpp-160) REVERT: A 111 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8098 (tm-30) REVERT: A 123 MET cc_start: 0.8607 (tpt) cc_final: 0.8363 (tmm) REVERT: A 124 ASN cc_start: 0.7527 (p0) cc_final: 0.7078 (p0) REVERT: A 140 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6215 (mtm-85) REVERT: A 169 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 173 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 181 GLU cc_start: 0.9569 (pp20) cc_final: 0.9363 (pp20) REVERT: A 199 TRP cc_start: 0.6833 (m-10) cc_final: 0.6578 (m-10) REVERT: A 249 PHE cc_start: 0.6611 (m-80) cc_final: 0.6326 (m-80) REVERT: A 374 ASN cc_start: 0.8977 (t0) cc_final: 0.8153 (p0) REVERT: A 380 LEU cc_start: 0.9028 (tp) cc_final: 0.8569 (mt) REVERT: B 198 LEU cc_start: 0.9200 (tp) cc_final: 0.8988 (tp) REVERT: B 215 GLN cc_start: 0.8621 (pt0) cc_final: 0.7976 (pp30) REVERT: B 235 PHE cc_start: 0.8946 (m-80) cc_final: 0.8702 (m-80) REVERT: B 251 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8587 (mt-10) REVERT: B 428 GLU cc_start: 0.8768 (mp0) cc_final: 0.8534 (mp0) REVERT: B 484 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8372 (mp) REVERT: B 579 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8296 (tpm-80) REVERT: C 172 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7801 (ptt-90) REVERT: C 173 ASP cc_start: 0.8993 (m-30) cc_final: 0.8776 (m-30) REVERT: C 195 ASP cc_start: 0.8147 (p0) cc_final: 0.7552 (p0) REVERT: C 197 SER cc_start: 0.9508 (t) cc_final: 0.9302 (p) REVERT: C 212 MET cc_start: 0.8938 (mmm) cc_final: 0.8076 (mmt) REVERT: C 244 ASP cc_start: 0.8599 (p0) cc_final: 0.8141 (p0) REVERT: C 245 PHE cc_start: 0.8759 (m-80) cc_final: 0.8534 (m-10) REVERT: C 356 ASP cc_start: 0.8446 (m-30) cc_final: 0.7979 (m-30) REVERT: C 518 ARG cc_start: 0.9199 (mtm110) cc_final: 0.8543 (mtm180) REVERT: C 525 MET cc_start: 0.8808 (mmm) cc_final: 0.8412 (mtp) REVERT: C 574 GLN cc_start: 0.8386 (tp-100) cc_final: 0.8048 (tp-100) REVERT: C 584 ASN cc_start: 0.8739 (t0) cc_final: 0.7813 (t0) REVERT: D 109 ASP cc_start: 0.8713 (t0) cc_final: 0.8357 (t0) REVERT: D 212 MET cc_start: 0.9458 (mmm) cc_final: 0.9184 (mmm) REVERT: D 214 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.6985 (m-10) REVERT: D 215 GLN cc_start: 0.9102 (tt0) cc_final: 0.8711 (tm-30) REVERT: D 272 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: D 299 GLU cc_start: 0.8466 (mp0) cc_final: 0.7732 (pp20) REVERT: D 398 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: D 463 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: H 41 VAL cc_start: 0.6420 (t) cc_final: 0.6126 (m) REVERT: H 60 TYR cc_start: 0.7781 (m-80) cc_final: 0.7400 (m-80) REVERT: H 69 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6660 (t70) REVERT: H 111 GLU cc_start: 0.7473 (pp20) cc_final: 0.6601 (pm20) REVERT: H 169 GLU cc_start: 0.9453 (tt0) cc_final: 0.9048 (tp30) REVERT: H 199 TRP cc_start: 0.8178 (t-100) cc_final: 0.7781 (t60) REVERT: H 243 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: H 244 THR cc_start: 0.7416 (OUTLIER) cc_final: 0.6977 (p) outliers start: 80 outliers final: 37 residues processed: 405 average time/residue: 0.4888 time to fit residues: 230.5864 Evaluate side-chains 386 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 244 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 48 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 62 optimal weight: 40.0000 chunk 144 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 474 ASN E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 345 GLN D 307 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.150571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.106663 restraints weight = 40579.322| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.38 r_work: 0.3350 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22542 Z= 0.165 Angle : 0.658 12.077 30697 Z= 0.335 Chirality : 0.044 0.246 3439 Planarity : 0.004 0.053 3904 Dihedral : 5.261 36.374 2910 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.45 % Allowed : 21.68 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2658 helix: 0.42 (0.26), residues: 383 sheet: -0.71 (0.18), residues: 786 loop : -0.01 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 63 TYR 0.029 0.002 TYR H 135 PHE 0.030 0.002 PHE A 110 TRP 0.021 0.001 TRP A 199 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (22454) covalent geometry : angle 0.65025 / 0.33 (30500) SS BOND : bond 0.00495 / 0.28 ( 31) SS BOND : angle 0.98913 / 0.72 ( 62) hydrogen bonds : bond 0.03609 / 2.33 ( 800) hydrogen bonds : angle 5.82236 / 4.09 ( 2013) metal coordination : bond 0.00344 / 0.31 ( 12) link_BETA1-4 : bond 0.00335 / 0.22 ( 22) link_BETA1-4 : angle 1.39413 / 1.02 ( 66) link_BETA1-6 : bond 0.00324 / 0.16 ( 4) link_BETA1-6 : angle 1.22228 / 0.84 ( 12) link_NAG-ASN : bond 0.00190 / 0.12 ( 19) link_NAG-ASN : angle 1.76892 / 1.18 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 362 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7911 (t0) cc_final: 0.6696 (m-30) REVERT: E 123 GLN cc_start: 0.8294 (mm110) cc_final: 0.7445 (mp10) REVERT: E 129 TRP cc_start: 0.7973 (p-90) cc_final: 0.7521 (p-90) REVERT: E 210 SER cc_start: 0.8633 (t) cc_final: 0.8345 (t) REVERT: E 215 GLN cc_start: 0.8040 (tt0) cc_final: 0.7445 (tm-30) REVERT: E 256 MET cc_start: 0.8521 (ttt) cc_final: 0.7747 (tmt) REVERT: E 263 HIS cc_start: 0.7916 (m-70) cc_final: 0.7509 (t70) REVERT: E 293 ASP cc_start: 0.8572 (t0) cc_final: 0.8265 (p0) REVERT: E 338 LYS cc_start: 0.9495 (mttm) cc_final: 0.9055 (mmtt) REVERT: E 364 ARG cc_start: 0.8779 (ptp-170) cc_final: 0.8098 (ptp90) REVERT: E 370 ASN cc_start: 0.8689 (t0) cc_final: 0.8372 (t0) REVERT: E 398 GLU cc_start: 0.7909 (pm20) cc_final: 0.7600 (pm20) REVERT: E 453 LYS cc_start: 0.8906 (pttt) cc_final: 0.8583 (ptmm) REVERT: E 471 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7837 (tm) REVERT: E 514 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7598 (mp0) REVERT: E 525 MET cc_start: 0.8491 (mmm) cc_final: 0.7976 (mtp) REVERT: E 586 ASP cc_start: 0.8036 (p0) cc_final: 0.7681 (p0) REVERT: A 63 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7348 (mtt180) REVERT: A 72 GLU cc_start: 0.6579 (tp30) cc_final: 0.6096 (mm-30) REVERT: A 111 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8093 (tm-30) REVERT: A 123 MET cc_start: 0.8614 (tpt) cc_final: 0.8403 (tmm) REVERT: A 124 ASN cc_start: 0.7539 (p0) cc_final: 0.7112 (p0) REVERT: A 140 ARG cc_start: 0.7387 (mtt180) cc_final: 0.6211 (mtm-85) REVERT: A 169 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 173 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8240 (mm-30) REVERT: A 199 TRP cc_start: 0.7076 (m-10) cc_final: 0.6845 (m-10) REVERT: A 247 GLU cc_start: 0.7006 (pm20) cc_final: 0.6626 (pm20) REVERT: A 249 PHE cc_start: 0.6616 (m-80) cc_final: 0.6345 (m-80) REVERT: A 374 ASN cc_start: 0.8980 (t0) cc_final: 0.8153 (p0) REVERT: A 380 LEU cc_start: 0.8995 (tp) cc_final: 0.8518 (mt) REVERT: B 198 LEU cc_start: 0.9217 (tp) cc_final: 0.8992 (tp) REVERT: B 215 GLN cc_start: 0.8576 (pt0) cc_final: 0.7931 (pp30) REVERT: B 235 PHE cc_start: 0.8919 (m-80) cc_final: 0.8695 (m-80) REVERT: B 251 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: B 266 LEU cc_start: 0.9152 (tp) cc_final: 0.8843 (mt) REVERT: B 281 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: B 334 ILE cc_start: 0.9017 (mp) cc_final: 0.8795 (mp) REVERT: B 428 GLU cc_start: 0.8725 (mp0) cc_final: 0.7646 (mp0) REVERT: B 453 LYS cc_start: 0.8391 (ptmm) cc_final: 0.7509 (tttp) REVERT: B 484 LEU cc_start: 0.8818 (mt) cc_final: 0.8350 (mp) REVERT: C 157 ILE cc_start: 0.8894 (mt) cc_final: 0.8667 (mt) REVERT: C 172 ARG cc_start: 0.8650 (ppt-90) cc_final: 0.7946 (ptt-90) REVERT: C 173 ASP cc_start: 0.8936 (m-30) cc_final: 0.8693 (m-30) REVERT: C 195 ASP cc_start: 0.8142 (p0) cc_final: 0.7560 (p0) REVERT: C 197 SER cc_start: 0.9526 (t) cc_final: 0.9315 (p) REVERT: C 212 MET cc_start: 0.8958 (mmm) cc_final: 0.7879 (mmt) REVERT: C 356 ASP cc_start: 0.8410 (m-30) cc_final: 0.7875 (m-30) REVERT: C 518 ARG cc_start: 0.9197 (mtm110) cc_final: 0.8527 (mtm180) REVERT: C 525 MET cc_start: 0.8816 (mmm) cc_final: 0.8524 (mtp) REVERT: C 574 GLN cc_start: 0.8268 (tp-100) cc_final: 0.7934 (tp-100) REVERT: C 584 ASN cc_start: 0.8686 (t0) cc_final: 0.7753 (t0) REVERT: D 109 ASP cc_start: 0.8749 (t0) cc_final: 0.8360 (t70) REVERT: D 212 MET cc_start: 0.9425 (mmm) cc_final: 0.9189 (mmm) REVERT: D 214 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: D 215 GLN cc_start: 0.9093 (tt0) cc_final: 0.8706 (tm-30) REVERT: D 272 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: D 299 GLU cc_start: 0.8394 (mp0) cc_final: 0.7669 (pp20) REVERT: D 398 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: D 463 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: D 492 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: H 41 VAL cc_start: 0.6439 (t) cc_final: 0.6176 (m) REVERT: H 60 TYR cc_start: 0.7792 (m-80) cc_final: 0.7444 (m-80) REVERT: H 69 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6457 (t70) REVERT: H 74 ARG cc_start: 0.7387 (mmt-90) cc_final: 0.7126 (mmt-90) REVERT: H 111 GLU cc_start: 0.7552 (pp20) cc_final: 0.6722 (pm20) REVERT: H 140 ARG cc_start: 0.7615 (mtt180) cc_final: 0.7310 (mpt-90) REVERT: H 169 GLU cc_start: 0.9458 (tt0) cc_final: 0.9056 (tp30) REVERT: H 199 TRP cc_start: 0.8182 (t-100) cc_final: 0.7788 (t60) REVERT: H 243 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.8026 (ttm-80) outliers start: 57 outliers final: 31 residues processed: 401 average time/residue: 0.5016 time to fit residues: 233.3256 Evaluate side-chains 388 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 255 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 8 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 189 HIS E 474 ASN E 584 ASN A 37 ASN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 505 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.147551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.102777 restraints weight = 40808.031| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.37 r_work: 0.3283 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 22542 Z= 0.309 Angle : 0.744 15.398 30697 Z= 0.380 Chirality : 0.047 0.295 3439 Planarity : 0.005 0.057 3904 Dihedral : 5.435 37.762 2910 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 2.84 % Allowed : 21.85 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.16), residues: 2658 helix: 0.31 (0.26), residues: 383 sheet: -0.78 (0.18), residues: 780 loop : -0.14 (0.17), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 578 TYR 0.026 0.002 TYR H 135 PHE 0.023 0.002 PHE A 121 TRP 0.021 0.002 TRP D 567 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.31 (22454) covalent geometry : angle 0.73603 / 0.38 (30500) SS BOND : bond 0.00664 / 0.40 ( 31) SS BOND : angle 1.11422 / 0.80 ( 62) hydrogen bonds : bond 0.03975 / 2.56 ( 800) hydrogen bonds : angle 5.97508 / 4.20 ( 2013) metal coordination : bond 0.00749 / 0.64 ( 12) link_BETA1-4 : bond 0.00305 / 0.20 ( 22) link_BETA1-4 : angle 1.52784 / 1.10 ( 66) link_BETA1-6 : bond 0.00196 / 0.10 ( 4) link_BETA1-6 : angle 1.76052 / 1.23 ( 12) link_NAG-ASN : bond 0.00329 / 0.20 ( 19) link_NAG-ASN : angle 1.85066 / 1.23 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 109 ASP cc_start: 0.7853 (t0) cc_final: 0.6588 (m-30) REVERT: E 120 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8467 (mt) REVERT: E 123 GLN cc_start: 0.8281 (mm110) cc_final: 0.7677 (mp10) REVERT: E 129 TRP cc_start: 0.7970 (p-90) cc_final: 0.7557 (p-90) REVERT: E 141 ILE cc_start: 0.8355 (mt) cc_final: 0.8103 (mt) REVERT: E 210 SER cc_start: 0.8713 (t) cc_final: 0.8470 (t) REVERT: E 215 GLN cc_start: 0.7963 (tt0) cc_final: 0.7369 (tm-30) REVERT: E 338 LYS cc_start: 0.9426 (mttm) cc_final: 0.8932 (mmtt) REVERT: E 364 ARG cc_start: 0.8813 (ptp-170) cc_final: 0.8577 (ptm160) REVERT: E 370 ASN cc_start: 0.8706 (t0) cc_final: 0.8292 (t0) REVERT: E 453 LYS cc_start: 0.8889 (pttt) cc_final: 0.8620 (ptmm) REVERT: E 471 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7886 (tm) REVERT: E 514 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7627 (mp0) REVERT: E 525 MET cc_start: 0.8417 (mmm) cc_final: 0.7705 (mtp) REVERT: E 567 TRP cc_start: 0.6748 (m-90) cc_final: 0.5284 (m-90) REVERT: E 586 ASP cc_start: 0.8138 (p0) cc_final: 0.7756 (p0) REVERT: A 63 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.7354 (mtt180) REVERT: A 72 GLU cc_start: 0.6553 (tp30) cc_final: 0.6154 (mm-30) REVERT: A 97 ARG cc_start: 0.7556 (tpm170) cc_final: 0.7172 (tpp-160) REVERT: A 168 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8543 (tm) REVERT: A 169 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 173 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 199 TRP cc_start: 0.7273 (m100) cc_final: 0.7009 (m-10) REVERT: A 213 GLU cc_start: 0.8928 (tp30) cc_final: 0.8719 (tp30) REVERT: A 374 ASN cc_start: 0.9014 (t0) cc_final: 0.8182 (p0) REVERT: A 380 LEU cc_start: 0.9038 (tp) cc_final: 0.8591 (mt) REVERT: B 198 LEU cc_start: 0.9285 (tp) cc_final: 0.9051 (tp) REVERT: B 214 TYR cc_start: 0.8742 (m-10) cc_final: 0.8512 (m-80) REVERT: B 215 GLN cc_start: 0.8622 (pt0) cc_final: 0.8006 (pp30) REVERT: B 235 PHE cc_start: 0.8966 (m-80) cc_final: 0.8744 (m-80) REVERT: B 428 GLU cc_start: 0.8793 (mp0) cc_final: 0.8539 (mp0) REVERT: B 453 LYS cc_start: 0.8272 (ptmm) cc_final: 0.7455 (tttp) REVERT: B 484 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 195 ASP cc_start: 0.8215 (p0) cc_final: 0.7591 (p0) REVERT: C 197 SER cc_start: 0.9561 (t) cc_final: 0.9337 (p) REVERT: C 212 MET cc_start: 0.8817 (mmm) cc_final: 0.7988 (mmt) REVERT: C 244 ASP cc_start: 0.8525 (p0) cc_final: 0.8049 (p0) REVERT: C 245 PHE cc_start: 0.8699 (m-10) cc_final: 0.8208 (m-10) REVERT: C 356 ASP cc_start: 0.8437 (m-30) cc_final: 0.7923 (m-30) REVERT: C 574 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8087 (tp-100) REVERT: C 584 ASN cc_start: 0.8763 (t0) cc_final: 0.7869 (t0) REVERT: D 109 ASP cc_start: 0.8709 (t0) cc_final: 0.8334 (t0) REVERT: D 214 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.6975 (m-10) REVERT: D 215 GLN cc_start: 0.9174 (tt0) cc_final: 0.8784 (tm-30) REVERT: D 272 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: D 398 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: D 444 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8519 (p) REVERT: D 463 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: D 498 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: H 41 VAL cc_start: 0.6496 (t) cc_final: 0.6217 (m) REVERT: H 60 TYR cc_start: 0.7924 (m-80) cc_final: 0.7493 (m-80) REVERT: H 69 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6462 (t70) REVERT: H 111 GLU cc_start: 0.7557 (pp20) cc_final: 0.6729 (pm20) REVERT: H 169 GLU cc_start: 0.9464 (tt0) cc_final: 0.9184 (tp30) REVERT: H 199 TRP cc_start: 0.8294 (t-100) cc_final: 0.7884 (t60) REVERT: H 243 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8089 (ttm-80) outliers start: 66 outliers final: 39 residues processed: 390 average time/residue: 0.4744 time to fit residues: 215.6472 Evaluate side-chains 383 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 550 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 350 MET Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 256 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 173 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 185 optimal weight: 0.3980 chunk 144 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 474 ASN E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 455 GLN D 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.150533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106817 restraints weight = 40624.340| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.38 r_work: 0.3340 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22542 Z= 0.151 Angle : 0.695 13.222 30697 Z= 0.352 Chirality : 0.044 0.285 3439 Planarity : 0.004 0.055 3904 Dihedral : 5.237 36.259 2910 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 2.28 % Allowed : 23.14 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2658 helix: 0.37 (0.26), residues: 383 sheet: -0.83 (0.18), residues: 771 loop : -0.08 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 578 TYR 0.026 0.002 TYR H 135 PHE 0.028 0.002 PHE A 110 TRP 0.027 0.001 TRP D 567 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (22454) covalent geometry : angle 0.68815 / 0.35 (30500) SS BOND : bond 0.00381 / 0.27 ( 31) SS BOND : angle 1.10949 / 0.80 ( 62) hydrogen bonds : bond 0.03661 / 2.39 ( 800) hydrogen bonds : angle 5.84231 / 4.12 ( 2013) metal coordination : bond 0.00284 / 0.24 ( 12) link_BETA1-4 : bond 0.00338 / 0.22 ( 22) link_BETA1-4 : angle 1.33525 / 0.97 ( 66) link_BETA1-6 : bond 0.00470 / 0.24 ( 4) link_BETA1-6 : angle 1.22648 / 0.85 ( 12) link_NAG-ASN : bond 0.00181 / 0.13 ( 19) link_NAG-ASN : angle 1.68268 / 1.11 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 359 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8808 (m-10) cc_final: 0.8257 (m-80) REVERT: E 120 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8502 (mt) REVERT: E 123 GLN cc_start: 0.8320 (mm110) cc_final: 0.7459 (mp10) REVERT: E 129 TRP cc_start: 0.7936 (p-90) cc_final: 0.7476 (p-90) REVERT: E 141 ILE cc_start: 0.8111 (mt) cc_final: 0.7770 (mt) REVERT: E 215 GLN cc_start: 0.8060 (tt0) cc_final: 0.7764 (tm-30) REVERT: E 273 LYS cc_start: 0.8001 (mmpt) cc_final: 0.7619 (mtmt) REVERT: E 293 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7340 (p0) REVERT: E 331 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8327 (mt-10) REVERT: E 338 LYS cc_start: 0.9320 (mttm) cc_final: 0.8915 (mmtt) REVERT: E 340 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8108 (mmmt) REVERT: E 364 ARG cc_start: 0.8797 (ptp-170) cc_final: 0.8562 (ptm160) REVERT: E 370 ASN cc_start: 0.8738 (t0) cc_final: 0.8322 (t0) REVERT: E 423 ASP cc_start: 0.8412 (m-30) cc_final: 0.8146 (m-30) REVERT: E 438 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7779 (m) REVERT: E 452 ASP cc_start: 0.9001 (m-30) cc_final: 0.8533 (p0) REVERT: E 453 LYS cc_start: 0.8878 (pttt) cc_final: 0.8597 (ptmm) REVERT: E 471 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7879 (tm) REVERT: E 474 ASN cc_start: 0.8739 (m-40) cc_final: 0.8485 (m110) REVERT: E 514 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7612 (mp0) REVERT: E 525 MET cc_start: 0.8314 (mmm) cc_final: 0.7713 (mtp) REVERT: E 567 TRP cc_start: 0.6781 (m-90) cc_final: 0.5440 (m-90) REVERT: E 586 ASP cc_start: 0.8129 (p0) cc_final: 0.7760 (p0) REVERT: A 63 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.7928 (mtt180) REVERT: A 74 ARG cc_start: 0.7207 (mpp-170) cc_final: 0.6293 (tpm170) REVERT: A 97 ARG cc_start: 0.7548 (tpm170) cc_final: 0.7237 (tpp-160) REVERT: A 111 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6837 (pp20) REVERT: A 123 MET cc_start: 0.8893 (tpt) cc_final: 0.7752 (pmm) REVERT: A 168 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8508 (tm) REVERT: A 169 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 173 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8219 (mm-30) REVERT: A 177 LYS cc_start: 0.8274 (tptp) cc_final: 0.7825 (tmmm) REVERT: A 181 GLU cc_start: 0.9631 (pp20) cc_final: 0.9142 (pm20) REVERT: A 213 GLU cc_start: 0.8895 (tp30) cc_final: 0.8640 (tp30) REVERT: A 247 GLU cc_start: 0.6626 (pm20) cc_final: 0.6258 (pm20) REVERT: A 249 PHE cc_start: 0.6641 (m-80) cc_final: 0.6439 (m-80) REVERT: A 374 ASN cc_start: 0.8973 (t0) cc_final: 0.8141 (p0) REVERT: A 380 LEU cc_start: 0.9024 (tp) cc_final: 0.8574 (mt) REVERT: B 214 TYR cc_start: 0.8581 (m-10) cc_final: 0.8281 (m-80) REVERT: B 215 GLN cc_start: 0.8544 (pt0) cc_final: 0.7941 (pp30) REVERT: B 235 PHE cc_start: 0.8914 (m-80) cc_final: 0.8701 (m-80) REVERT: B 266 LEU cc_start: 0.9123 (tp) cc_final: 0.8847 (mt) REVERT: B 281 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: B 334 ILE cc_start: 0.9014 (mp) cc_final: 0.8804 (mp) REVERT: B 428 GLU cc_start: 0.8718 (mp0) cc_final: 0.7577 (mp0) REVERT: B 453 LYS cc_start: 0.8348 (ptmm) cc_final: 0.7809 (tttp) REVERT: B 484 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8312 (mp) REVERT: C 193 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8433 (m) REVERT: C 195 ASP cc_start: 0.8196 (p0) cc_final: 0.7606 (p0) REVERT: C 197 SER cc_start: 0.9566 (t) cc_final: 0.9335 (p) REVERT: C 212 MET cc_start: 0.8953 (mmm) cc_final: 0.8057 (mmt) REVERT: C 244 ASP cc_start: 0.8345 (p0) cc_final: 0.7776 (p0) REVERT: C 356 ASP cc_start: 0.8396 (m-30) cc_final: 0.7924 (m-30) REVERT: C 574 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7919 (tp-100) REVERT: C 584 ASN cc_start: 0.8705 (t0) cc_final: 0.7827 (t0) REVERT: D 109 ASP cc_start: 0.8803 (t0) cc_final: 0.8393 (t70) REVERT: D 181 ASP cc_start: 0.8906 (p0) cc_final: 0.8678 (p0) REVERT: D 214 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.6864 (m-10) REVERT: D 215 GLN cc_start: 0.9127 (tt0) cc_final: 0.8792 (tm-30) REVERT: D 272 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: D 299 GLU cc_start: 0.8413 (mp0) cc_final: 0.7613 (pp20) REVERT: D 398 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: D 463 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: H 41 VAL cc_start: 0.6554 (t) cc_final: 0.6262 (m) REVERT: H 60 TYR cc_start: 0.8009 (m-80) cc_final: 0.7544 (m-80) REVERT: H 69 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6482 (t70) REVERT: H 72 GLU cc_start: -0.0618 (pm20) cc_final: -0.0886 (pm20) REVERT: H 75 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.6521 (mpt90) REVERT: H 111 GLU cc_start: 0.7410 (pp20) cc_final: 0.6653 (pm20) REVERT: H 128 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7144 (mmm160) REVERT: H 140 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7437 (mpt-90) REVERT: H 199 TRP cc_start: 0.8163 (t-100) cc_final: 0.7761 (t60) REVERT: H 243 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: H 244 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7131 (p) REVERT: H 247 GLU cc_start: 0.5171 (mm-30) cc_final: 0.4582 (mm-30) outliers start: 53 outliers final: 23 residues processed: 392 average time/residue: 0.5286 time to fit residues: 241.0022 Evaluate side-chains 379 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 342 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 186 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 243 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 247 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 584 ASN A 37 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN B 370 ASN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN D 307 GLN H 71 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105196 restraints weight = 40917.026| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.34 r_work: 0.3331 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22542 Z= 0.209 Angle : 0.725 15.927 30697 Z= 0.365 Chirality : 0.045 0.274 3439 Planarity : 0.004 0.054 3904 Dihedral : 5.261 36.275 2910 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.15 % Allowed : 23.70 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2658 helix: 0.33 (0.26), residues: 383 sheet: -0.72 (0.19), residues: 741 loop : -0.19 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 69 TYR 0.025 0.002 TYR H 135 PHE 0.028 0.002 PHE H 249 TRP 0.061 0.002 TRP A 199 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (22454) covalent geometry : angle 0.71853 / 0.36 (30500) SS BOND : bond 0.00462 / 0.30 ( 31) SS BOND : angle 1.06402 / 0.76 ( 62) hydrogen bonds : bond 0.03778 / 2.45 ( 800) hydrogen bonds : angle 5.87264 / 4.14 ( 2013) metal coordination : bond 0.00439 / 0.39 ( 12) link_BETA1-4 : bond 0.00314 / 0.20 ( 22) link_BETA1-4 : angle 1.38492 / 0.99 ( 66) link_BETA1-6 : bond 0.00214 / 0.11 ( 4) link_BETA1-6 : angle 1.48113 / 1.04 ( 12) link_NAG-ASN : bond 0.00253 / 0.16 ( 19) link_NAG-ASN : angle 1.67657 / 1.12 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5316 Ramachandran restraints generated. 2658 Oldfield, 0 Emsley, 2658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 348 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 PHE cc_start: 0.8839 (m-10) cc_final: 0.8332 (m-80) REVERT: E 120 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8435 (mt) REVERT: E 123 GLN cc_start: 0.8259 (mm110) cc_final: 0.7491 (mp-120) REVERT: E 129 TRP cc_start: 0.8133 (p-90) cc_final: 0.7676 (p-90) REVERT: E 141 ILE cc_start: 0.8142 (mt) cc_final: 0.7808 (mt) REVERT: E 215 GLN cc_start: 0.7978 (tt0) cc_final: 0.7701 (tm-30) REVERT: E 293 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7573 (p0) REVERT: E 331 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8367 (mt-10) REVERT: E 338 LYS cc_start: 0.9364 (mttm) cc_final: 0.8942 (mmtt) REVERT: E 340 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8051 (mmmt) REVERT: E 364 ARG cc_start: 0.8767 (ptp-170) cc_final: 0.8528 (ptm160) REVERT: E 370 ASN cc_start: 0.8668 (t0) cc_final: 0.8089 (t0) REVERT: E 423 ASP cc_start: 0.8372 (m-30) cc_final: 0.8116 (m-30) REVERT: E 453 LYS cc_start: 0.8881 (pttt) cc_final: 0.8599 (ptmm) REVERT: E 471 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7819 (tm) REVERT: E 514 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7661 (mp0) REVERT: E 525 MET cc_start: 0.8324 (mmm) cc_final: 0.7692 (mtp) REVERT: E 567 TRP cc_start: 0.6859 (m-90) cc_final: 0.5389 (m-90) REVERT: E 586 ASP cc_start: 0.8135 (p0) cc_final: 0.7773 (p0) REVERT: A 63 ARG cc_start: 0.8767 (mtp-110) cc_final: 0.7949 (mtt180) REVERT: A 72 GLU cc_start: 0.6298 (mm-30) cc_final: 0.5382 (tp30) REVERT: A 74 ARG cc_start: 0.7303 (mpp-170) cc_final: 0.6623 (tpm170) REVERT: A 82 PHE cc_start: 0.7849 (m-80) cc_final: 0.7214 (m-80) REVERT: A 97 ARG cc_start: 0.7570 (tpm170) cc_final: 0.7166 (tpp-160) REVERT: A 111 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7120 (pp20) REVERT: A 168 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8501 (tm) REVERT: A 169 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 173 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 179 ASN cc_start: 0.9562 (m-40) cc_final: 0.9230 (m110) REVERT: A 213 GLU cc_start: 0.8657 (tp30) cc_final: 0.8412 (tp30) REVERT: A 247 GLU cc_start: 0.7270 (pm20) cc_final: 0.7062 (pm20) REVERT: A 374 ASN cc_start: 0.8981 (t0) cc_final: 0.8122 (p0) REVERT: A 380 LEU cc_start: 0.9045 (tp) cc_final: 0.8594 (mt) REVERT: B 214 TYR cc_start: 0.8705 (m-10) cc_final: 0.8395 (m-80) REVERT: B 215 GLN cc_start: 0.8540 (pt0) cc_final: 0.7849 (pp30) REVERT: B 235 PHE cc_start: 0.8945 (m-80) cc_final: 0.8722 (m-80) REVERT: B 281 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: B 334 ILE cc_start: 0.9056 (mp) cc_final: 0.8822 (mp) REVERT: B 428 GLU cc_start: 0.8746 (mp0) cc_final: 0.8377 (mp0) REVERT: B 453 LYS cc_start: 0.8340 (ptmm) cc_final: 0.7790 (tttp) REVERT: B 484 LEU cc_start: 0.8829 (mt) cc_final: 0.8363 (mp) REVERT: C 195 ASP cc_start: 0.8216 (p0) cc_final: 0.7622 (p0) REVERT: C 197 SER cc_start: 0.9576 (t) cc_final: 0.9344 (p) REVERT: C 212 MET cc_start: 0.8955 (mmm) cc_final: 0.8063 (mmt) REVERT: C 244 ASP cc_start: 0.8486 (p0) cc_final: 0.7995 (p0) REVERT: C 356 ASP cc_start: 0.8408 (m-30) cc_final: 0.7938 (m-30) REVERT: C 574 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7926 (tp-100) REVERT: C 584 ASN cc_start: 0.8761 (t0) cc_final: 0.7904 (t0) REVERT: D 109 ASP cc_start: 0.8825 (t0) cc_final: 0.8515 (t0) REVERT: D 214 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: D 215 GLN cc_start: 0.9114 (tt0) cc_final: 0.8770 (tm-30) REVERT: D 272 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: D 299 GLU cc_start: 0.8461 (mp0) cc_final: 0.7629 (pp20) REVERT: D 398 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: D 463 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: H 41 VAL cc_start: 0.6477 (t) cc_final: 0.6201 (m) REVERT: H 60 TYR cc_start: 0.7986 (m-80) cc_final: 0.7606 (m-80) REVERT: H 69 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6426 (t70) REVERT: H 74 ARG cc_start: 0.6860 (mmt-90) cc_final: 0.6472 (mmt-90) REVERT: H 75 ARG cc_start: 0.7421 (mmt-90) cc_final: 0.6310 (mpt90) REVERT: H 111 GLU cc_start: 0.7417 (pp20) cc_final: 0.6648 (pm20) REVERT: H 128 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7119 (mmm160) REVERT: H 140 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7380 (mpt-90) REVERT: H 149 MET cc_start: 0.8624 (tmm) cc_final: 0.8327 (tmm) REVERT: H 199 TRP cc_start: 0.8152 (t-100) cc_final: 0.7766 (t60) REVERT: H 243 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8169 (ttm-80) REVERT: H 244 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.6951 (p) REVERT: H 247 GLU cc_start: 0.5087 (mm-30) cc_final: 0.4578 (mm-30) REVERT: H 347 GLU cc_start: 0.7861 (pm20) cc_final: 0.7332 (tp30) outliers start: 50 outliers final: 34 residues processed: 384 average time/residue: 0.5214 time to fit residues: 233.9771 Evaluate side-chains 379 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 334 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 262 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 244 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 159 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 584 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN ** B 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN D 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.148288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103841 restraints weight = 40932.222| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.39 r_work: 0.3306 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22542 Z= 0.251 Angle : 0.739 15.050 30697 Z= 0.375 Chirality : 0.046 0.279 3439 Planarity : 0.004 0.053 3904 Dihedral : 5.316 36.765 2910 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.82 % Rotamer: Outliers : 2.49 % Allowed : 23.66 % Favored : 73.85 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2658 helix: 0.25 (0.26), residues: 383 sheet: -0.82 (0.19), residues: 758 loop : -0.20 (0.17), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 69 TYR 0.024 0.002 TYR H 135 PHE 0.026 0.002 PHE H 249 TRP 0.073 0.002 TRP A 199 HIS 0.013 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (22454) covalent geometry : angle 0.73308 / 0.37 (30500) SS BOND : bond 0.00493 / 0.33 ( 31) SS BOND : angle 1.13898 / 0.80 ( 62) hydrogen bonds : bond 0.03833 / 2.48 ( 800) hydrogen bonds : angle 5.92116 / 4.18 ( 2013) metal coordination : bond 0.00521 / 0.44 ( 12) link_BETA1-4 : bond 0.00305 / 0.20 ( 22) link_BETA1-4 : angle 1.38378 / 0.99 ( 66) link_BETA1-6 : bond 0.00202 / 0.11 ( 4) link_BETA1-6 : angle 1.51211 / 1.08 ( 12) link_NAG-ASN : bond 0.00257 / 0.16 ( 19) link_NAG-ASN : angle 1.65507 / 1.11 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8349.04 seconds wall clock time: 143 minutes 12.27 seconds (8592.27 seconds total)