Starting phenix.real_space_refine on Sat Mar 7 14:45:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czl_30511/03_2026/7czl_30511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czl_30511/03_2026/7czl_30511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7czl_30511/03_2026/7czl_30511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czl_30511/03_2026/7czl_30511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7czl_30511/03_2026/7czl_30511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czl_30511/03_2026/7czl_30511.map" } resolution = 3.78 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2658 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 P 2 5.49 5 Mg 70 5.21 5 S 140 5.16 5 Cl 2 4.86 5 C 28272 2.51 5 N 5784 2.21 5 O 6583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40859 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2533 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 310} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3784 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 31, 'TRANS': 452} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3412 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 421} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2693 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 323} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 242 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 277 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "K" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 289 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 32} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 258 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "T" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 254 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 442 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "a" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2523 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 308} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3780 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 452} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "c" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3412 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 421} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "d" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2687 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 323} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 522 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 219 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "h" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 277 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "k" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 264 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 3, 'TRANS': 30} Chain: "l" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "m" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 258 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "t" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 254 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 442 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 215 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "n" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "y" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 215 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "X" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "x" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 254 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "A" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 551 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 4, 'LHG': 1, 'LMT': 1, 'MGE': 1, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1170 Unusual residues: {'BCR': 2, 'CLA': 16, 'LMT': 1, 'MGE': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-4': 1, 'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1100 Unusual residues: {' CA': 1, 'BCR': 3, 'CLA': 13, 'DGD': 3, 'MGE': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 455 Unusual residues: {'BCR': 1, 'CLA': 2, 'FE2': 1, 'MGE': 3, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "M" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'BCR': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 545 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 4, 'DGD': 1, 'LHG': 1, 'LMT': 1, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PQ9:plan-2': 1, 'PQ9:plan-3': 1, 'PQ9:plan-4': 1} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1153 Unusual residues: {'BCR': 3, 'CLA': 16, 'MGE': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-4': 2, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 16 Chain: "c" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 938 Unusual residues: {' CA': 1, 'BCR': 2, 'CLA': 12, 'DGD': 2, 'MGE': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 455 Unusual residues: {'BCR': 1, 'CLA': 2, 'FE2': 1, 'MGE': 3, 'PHO': 1, 'PQ9': 1, 'SQD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'BCR': 1, 'DGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "k" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'MGE': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "m" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'LMT': 1, 'MGE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 PQ9 a5407 " occ=0.50 ... (28 atoms not shown) pdb=" O4 PQ9 a5407 " occ=0.50 Time building chain proxies: 9.48, per 1000 atoms: 0.23 Number of scatterers: 40859 At special positions: 0 Unit cell: (199.901, 160.704, 109.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 Cl 2 17.00 S 140 16.00 P 2 15.00 Mg 70 11.99 O 6583 8.00 N 5784 7.00 C 28272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=72, symmetry=0 Number of additional bonds: simple=72, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7784 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 9 sheets defined 64.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.525A pdb=" N ARG A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.922A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix removed outlier: 3.554A pdb=" N ALA A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 135 removed outlier: 3.866A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.893A pdb=" N ILE A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.757A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 removed outlier: 3.879A pdb=" N ALA A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.649A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.601A pdb=" N ALA A 263 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 264 " --> pdb=" O GLN A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 260 through 264' Processing helix chain 'A' and resid 267 through 295 removed outlier: 3.767A pdb=" N PHE A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.560A pdb=" N PHE A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 removed outlier: 3.910A pdb=" N ILE A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 13 removed outlier: 3.507A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 44 removed outlier: 3.503A pdb=" N ALA B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.847A pdb=" N MET B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 removed outlier: 4.117A pdb=" N ARG B 124 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 removed outlier: 3.627A pdb=" N ILE B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.680A pdb=" N PHE B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.260A pdb=" N VAL B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 258 removed outlier: 3.981A pdb=" N VAL B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 250 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 4.130A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 removed outlier: 4.274A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.900A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.551A pdb=" N VAL B 417 " --> pdb=" O ASP B 413 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.702A pdb=" N THR B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.962A pdb=" N PHE B 479 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 45 through 75 removed outlier: 3.696A pdb=" N GLY C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 removed outlier: 3.737A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 85' Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 108 through 134 removed outlier: 3.644A pdb=" N GLY C 115 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 removed outlier: 4.753A pdb=" N TYR C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 144' Processing helix chain 'C' and resid 155 through 181 removed outlier: 3.634A pdb=" N PHE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.715A pdb=" N LEU C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 253 removed outlier: 4.401A pdb=" N VAL C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 239 " --> pdb=" O GLY C 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 removed outlier: 3.610A pdb=" N ALA C 263 " --> pdb=" O TRP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 292 removed outlier: 3.800A pdb=" N LEU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 305 through 324 removed outlier: 3.649A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.104A pdb=" N LEU C 369 " --> pdb=" O TRP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.664A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 398 removed outlier: 3.796A pdb=" N GLU C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 390 " --> pdb=" O PRO C 386 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 397 " --> pdb=" O ALA C 393 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 454 removed outlier: 3.864A pdb=" N ALA C 427 " --> pdb=" O ARG C 423 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 458 Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 31 through 54 removed outlier: 3.821A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix removed outlier: 3.853A pdb=" N THR D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.013A pdb=" N THR D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.505A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 174 through 189 removed outlier: 3.851A pdb=" N PHE D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 221 removed outlier: 3.632A pdb=" N GLY D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 removed outlier: 3.545A pdb=" N ALA D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 256 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.829A pdb=" N GLY D 285 " --> pdb=" O MET D 281 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 334 removed outlier: 3.575A pdb=" N LEU D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 21 through 24 removed outlier: 4.017A pdb=" N SER E 24 " --> pdb=" O VAL E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 25 through 40 removed outlier: 3.678A pdb=" N ALA E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 48 removed outlier: 4.211A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.895A pdb=" N GLU E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU E 83 " --> pdb=" O PHE E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 42 removed outlier: 3.617A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL F 28 " --> pdb=" O HIS F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.700A pdb=" N GLY F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA F 36 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 12 removed outlier: 3.543A pdb=" N ARG H 12 " --> pdb=" O GLY H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 50 Processing helix chain 'I' and resid 2 through 25 removed outlier: 3.874A pdb=" N PHE I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE I 23 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 24 Processing helix chain 'K' and resid 27 through 44 removed outlier: 3.516A pdb=" N LEU K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE K 37 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL K 43 " --> pdb=" O TRP K 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 37 removed outlier: 3.983A pdb=" N GLY L 20 " --> pdb=" O SER L 16 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 32 removed outlier: 3.745A pdb=" N ALA M 10 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR M 11 " --> pdb=" O GLY M 7 " (cutoff:3.500A) Proline residue: M 18 - end of helix removed outlier: 3.648A pdb=" N LEU M 25 " --> pdb=" O PHE M 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 removed outlier: 3.854A pdb=" N TYR T 6 " --> pdb=" O GLU T 2 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE T 19 " --> pdb=" O ALA T 15 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE T 22 " --> pdb=" O PHE T 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 29 removed outlier: 3.684A pdb=" N VAL Z 13 " --> pdb=" O LEU Z 9 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.920A pdb=" N SER Z 29 " --> pdb=" O VAL Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 37 Processing helix chain 'Z' and resid 38 through 62 removed outlier: 3.854A pdb=" N GLY Z 45 " --> pdb=" O PHE Z 41 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL Z 51 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Z 52 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL Z 54 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY Z 55 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL Z 56 " --> pdb=" O LEU Z 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU Z 57 " --> pdb=" O VAL Z 53 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE Z 60 " --> pdb=" O VAL Z 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 5013 through 5023 Processing helix chain 'a' and resid 5031 through 5054 removed outlier: 3.922A pdb=" N ILE a5036 " --> pdb=" O TRP a5032 " (cutoff:3.500A) Proline residue: a5039 - end of helix removed outlier: 3.554A pdb=" N ALA a5051 " --> pdb=" O CYS a5047 " (cutoff:3.500A) Processing helix chain 'a' and resid 5101 through 5108 Processing helix chain 'a' and resid 5109 through 5135 removed outlier: 3.865A pdb=" N GLN a5113 " --> pdb=" O GLY a5109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE a5117 " --> pdb=" O GLN a5113 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS a5125 " --> pdb=" O LEU a5121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP a5131 " --> pdb=" O MET a5127 " (cutoff:3.500A) Processing helix chain 'a' and resid 5142 through 5158 removed outlier: 4.131A pdb=" N ALA a5149 " --> pdb=" O VAL a5145 " (cutoff:3.500A) Proline residue: a5150 - end of helix Processing helix chain 'a' and resid 5159 through 5166 removed outlier: 3.893A pdb=" N ILE a5163 " --> pdb=" O LEU a5159 " (cutoff:3.500A) Processing helix chain 'a' and resid 5167 through 5171 Processing helix chain 'a' and resid 5176 through 5191 removed outlier: 3.757A pdb=" N PHE a5180 " --> pdb=" O ILE a5176 " (cutoff:3.500A) Processing helix chain 'a' and resid 5195 through 5222 removed outlier: 3.878A pdb=" N ALA a5203 " --> pdb=" O GLN a5199 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL a5219 " --> pdb=" O HIS a5215 " (cutoff:3.500A) Processing helix chain 'a' and resid 5247 through 5259 removed outlier: 3.649A pdb=" N GLY a5253 " --> pdb=" O VAL a5249 " (cutoff:3.500A) Processing helix chain 'a' and resid 5260 through 5264 removed outlier: 3.600A pdb=" N ALA a5263 " --> pdb=" O PHE a5260 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER a5264 " --> pdb=" O GLN a5261 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 5260 through 5264' Processing helix chain 'a' and resid 5267 through 5295 removed outlier: 3.767A pdb=" N PHE a5273 " --> pdb=" O ARG a5269 " (cutoff:3.500A) Proline residue: a5279 - end of helix removed outlier: 3.561A pdb=" N PHE a5285 " --> pdb=" O VAL a5281 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR a5286 " --> pdb=" O GLY a5282 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER a5291 " --> pdb=" O ALA a5287 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE a5295 " --> pdb=" O SER a5291 " (cutoff:3.500A) Processing helix chain 'a' and resid 5316 through 5333 removed outlier: 3.910A pdb=" N ILE a5320 " --> pdb=" O THR a5316 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL a5330 " --> pdb=" O LEU a5326 " (cutoff:3.500A) Processing helix chain 'b' and resid 5007 through 5013 removed outlier: 3.506A pdb=" N VAL b5011 " --> pdb=" O VAL b5008 " (cutoff:3.500A) Processing helix chain 'b' and resid 5015 through 5044 removed outlier: 3.503A pdb=" N ALA b5038 " --> pdb=" O ALA b5034 " (cutoff:3.500A) Processing helix chain 'b' and resid 5062 through 5069 removed outlier: 3.847A pdb=" N MET b5066 " --> pdb=" O VAL b5062 " (cutoff:3.500A) Processing helix chain 'b' and resid 5092 through 5117 Processing helix chain 'b' and resid 5120 through 5124 removed outlier: 4.118A pdb=" N ARG b5124 " --> pdb=" O GLU b5121 " (cutoff:3.500A) Processing helix chain 'b' and resid 5134 through 5156 removed outlier: 3.627A pdb=" N ILE b5141 " --> pdb=" O LYS b5137 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS b5142 " --> pdb=" O MET b5138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b5148 " --> pdb=" O PHE b5144 " (cutoff:3.500A) Processing helix chain 'b' and resid 5186 through 5191 removed outlier: 3.679A pdb=" N PHE b5190 " --> pdb=" O PRO b5187 " (cutoff:3.500A) Processing helix chain 'b' and resid 5194 through 5219 removed outlier: 4.259A pdb=" N VAL b5198 " --> pdb=" O ASN b5194 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA b5200 " --> pdb=" O GLY b5196 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b5207 " --> pdb=" O ILE b5203 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE b5217 " --> pdb=" O GLY b5213 " (cutoff:3.500A) Processing helix chain 'b' and resid 5222 through 5230 Processing helix chain 'b' and resid 5233 through 5258 removed outlier: 3.982A pdb=" N VAL b5237 " --> pdb=" O ASN b5233 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE b5250 " --> pdb=" O PHE b5246 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL b5251 " --> pdb=" O PHE b5247 " (cutoff:3.500A) Processing helix chain 'b' and resid 5271 through 5277 removed outlier: 4.130A pdb=" N TRP b5275 " --> pdb=" O THR b5271 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP b5276 " --> pdb=" O ARG b5272 " (cutoff:3.500A) Processing helix chain 'b' and resid 5278 through 5295 removed outlier: 4.273A pdb=" N ARG b5287 " --> pdb=" O GLU b5283 " (cutoff:3.500A) Processing helix chain 'b' and resid 5297 through 5304 Processing helix chain 'b' and resid 5306 through 5312 Processing helix chain 'b' and resid 5330 through 5335 removed outlier: 3.899A pdb=" N ASP b5334 " --> pdb=" O MET b5330 " (cutoff:3.500A) Processing helix chain 'b' and resid 5391 through 5396 Processing helix chain 'b' and resid 5413 through 5425 removed outlier: 3.550A pdb=" N VAL b5417 " --> pdb=" O ASP b5413 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE b5425 " --> pdb=" O ALA b5421 " (cutoff:3.500A) Processing helix chain 'b' and resid 5446 through 5475 removed outlier: 3.703A pdb=" N THR b5452 " --> pdb=" O ARG b5448 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE b5464 " --> pdb=" O LEU b5460 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS b5469 " --> pdb=" O GLY b5465 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU b5474 " --> pdb=" O GLY b5470 " (cutoff:3.500A) Processing helix chain 'b' and resid 5476 through 5481 removed outlier: 3.963A pdb=" N PHE b5479 " --> pdb=" O ARG b5476 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER b5480 " --> pdb=" O ASP b5477 " (cutoff:3.500A) Processing helix chain 'c' and resid 5037 through 5043 Processing helix chain 'c' and resid 5045 through 5075 removed outlier: 3.697A pdb=" N GLY c5051 " --> pdb=" O GLY c5047 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS c5074 " --> pdb=" O PHE c5070 " (cutoff:3.500A) Processing helix chain 'c' and resid 5080 through 5085 removed outlier: 3.737A pdb=" N GLN c5084 " --> pdb=" O PRO c5080 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY c5085 " --> pdb=" O MET c5081 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 5080 through 5085' Processing helix chain 'c' and resid 5088 through 5095 Processing helix chain 'c' and resid 5100 through 5104 Processing helix chain 'c' and resid 5108 through 5134 removed outlier: 3.644A pdb=" N GLY c5115 " --> pdb=" O PHE c5111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE c5127 " --> pdb=" O ALA c5123 " (cutoff:3.500A) Processing helix chain 'c' and resid 5139 through 5144 removed outlier: 4.754A pdb=" N TYR c5143 " --> pdb=" O THR c5139 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER c5144 " --> pdb=" O LEU c5140 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 5139 through 5144' Processing helix chain 'c' and resid 5155 through 5181 removed outlier: 3.634A pdb=" N PHE c5163 " --> pdb=" O THR c5159 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA c5172 " --> pdb=" O LEU c5168 " (cutoff:3.500A) Processing helix chain 'c' and resid 5209 through 5214 removed outlier: 3.715A pdb=" N LEU c5214 " --> pdb=" O PHE c5210 " (cutoff:3.500A) Processing helix chain 'c' and resid 5229 through 5253 removed outlier: 4.401A pdb=" N VAL c5233 " --> pdb=" O ASN c5229 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL c5234 " --> pdb=" O LEU c5230 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP c5239 " --> pdb=" O GLY c5235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA c5246 " --> pdb=" O LEU c5242 " (cutoff:3.500A) Processing helix chain 'c' and resid 5257 through 5263 removed outlier: 3.610A pdb=" N ALA c5263 " --> pdb=" O TRP c5259 " (cutoff:3.500A) Processing helix chain 'c' and resid 5267 through 5292 removed outlier: 3.799A pdb=" N LEU c5272 " --> pdb=" O GLY c5268 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL c5290 " --> pdb=" O ALA c5286 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP c5291 " --> pdb=" O THR c5287 " (cutoff:3.500A) Processing helix chain 'c' and resid 5298 through 5303 Processing helix chain 'c' and resid 5305 through 5324 removed outlier: 3.650A pdb=" N SER c5310 " --> pdb=" O GLY c5306 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU c5324 " --> pdb=" O ARG c5320 " (cutoff:3.500A) Processing helix chain 'c' and resid 5353 through 5358 Processing helix chain 'c' and resid 5365 through 5370 removed outlier: 4.104A pdb=" N LEU c5369 " --> pdb=" O TRP c5365 " (cutoff:3.500A) Processing helix chain 'c' and resid 5376 through 5384 removed outlier: 3.663A pdb=" N ASN c5382 " --> pdb=" O ASN c5378 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE c5384 " --> pdb=" O ILE c5380 " (cutoff:3.500A) Processing helix chain 'c' and resid 5385 through 5398 removed outlier: 3.795A pdb=" N GLU c5389 " --> pdb=" O GLN c5385 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG c5390 " --> pdb=" O PRO c5386 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET c5396 " --> pdb=" O ALA c5392 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR c5397 " --> pdb=" O ALA c5393 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS c5398 " --> pdb=" O GLU c5394 " (cutoff:3.500A) Processing helix chain 'c' and resid 5421 through 5454 removed outlier: 3.864A pdb=" N ALA c5427 " --> pdb=" O ARG c5423 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY c5446 " --> pdb=" O LEU c5442 " (cutoff:3.500A) Processing helix chain 'c' and resid 5455 through 5458 Processing helix chain 'd' and resid 5014 through 5023 Processing helix chain 'd' and resid 5031 through 5054 removed outlier: 3.822A pdb=" N LEU d5036 " --> pdb=" O TRP d5032 " (cutoff:3.500A) Proline residue: d5039 - end of helix removed outlier: 3.853A pdb=" N THR d5050 " --> pdb=" O GLY d5046 " (cutoff:3.500A) Processing helix chain 'd' and resid 5101 through 5107 Processing helix chain 'd' and resid 5108 through 5137 removed outlier: 4.014A pdb=" N THR d5112 " --> pdb=" O GLY d5108 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA d5133 " --> pdb=" O GLN d5129 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG d5134 " --> pdb=" O PHE d5130 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU d5135 " --> pdb=" O GLU d5131 " (cutoff:3.500A) Processing helix chain 'd' and resid 5140 through 5158 removed outlier: 3.505A pdb=" N ILE d5144 " --> pdb=" O PRO d5140 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA d5148 " --> pdb=" O ILE d5144 " (cutoff:3.500A) Proline residue: d5149 - end of helix Processing helix chain 'd' and resid 5158 through 5163 Processing helix chain 'd' and resid 5174 through 5189 removed outlier: 3.851A pdb=" N PHE d5179 " --> pdb=" O VAL d5175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE d5184 " --> pdb=" O ARG d5180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE d5185 " --> pdb=" O PHE d5181 " (cutoff:3.500A) Processing helix chain 'd' and resid 5194 through 5221 removed outlier: 3.632A pdb=" N GLY d5200 " --> pdb=" O PHE d5196 " (cutoff:3.500A) Processing helix chain 'd' and resid 5245 through 5256 removed outlier: 3.545A pdb=" N ALA d5249 " --> pdb=" O SER d5245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE d5256 " --> pdb=" O PHE d5252 " (cutoff:3.500A) Processing helix chain 'd' and resid 5263 through 5291 Proline residue: d5275 - end of helix removed outlier: 3.829A pdb=" N GLY d5285 " --> pdb=" O MET d5281 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL d5287 " --> pdb=" O ALA d5283 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU d5291 " --> pdb=" O VAL d5287 " (cutoff:3.500A) Processing helix chain 'd' and resid 5298 through 5306 Processing helix chain 'd' and resid 5315 through 5334 removed outlier: 3.577A pdb=" N LEU d5320 " --> pdb=" O THR d5316 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG d5326 " --> pdb=" O ASN d5322 " (cutoff:3.500A) Proline residue: d5331 - end of helix Processing helix chain 'e' and resid 5021 through 5024 removed outlier: 4.017A pdb=" N SER e5024 " --> pdb=" O VAL e5021 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 5021 through 5024' Processing helix chain 'e' and resid 5025 through 5040 removed outlier: 3.679A pdb=" N ALA e5033 " --> pdb=" O ALA e5029 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY e5034 " --> pdb=" O LEU e5030 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL e5038 " --> pdb=" O GLY e5034 " (cutoff:3.500A) Processing helix chain 'e' and resid 5041 through 5048 removed outlier: 4.210A pdb=" N ASP e5045 " --> pdb=" O GLY e5041 " (cutoff:3.500A) Processing helix chain 'e' and resid 5071 through 5083 removed outlier: 3.842A pdb=" N GLU e5077 " --> pdb=" O LYS e5073 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR e5078 " --> pdb=" O GLN e5074 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE e5079 " --> pdb=" O GLN e5075 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU e5083 " --> pdb=" O PHE e5079 " (cutoff:3.500A) Processing helix chain 'f' and resid 5018 through 5042 removed outlier: 3.538A pdb=" N ALA f5022 " --> pdb=" O VAL f5018 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL f5023 " --> pdb=" O ARG f5019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL f5028 " --> pdb=" O HIS f5024 " (cutoff:3.500A) Proline residue: f5029 - end of helix removed outlier: 3.701A pdb=" N GLY f5035 " --> pdb=" O ILE f5031 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA f5036 " --> pdb=" O PHE f5032 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE f5042 " --> pdb=" O ALA f5038 " (cutoff:3.500A) Processing helix chain 'h' and resid 5005 through 5012 removed outlier: 3.543A pdb=" N ARG h5012 " --> pdb=" O GLY h5008 " (cutoff:3.500A) Processing helix chain 'h' and resid 5028 through 5050 Processing helix chain 'i' and resid 5002 through 5025 removed outlier: 3.874A pdb=" N PHE i5021 " --> pdb=" O LEU i5017 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY i5022 " --> pdb=" O LEU i5018 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE i5023 " --> pdb=" O PHE i5019 " (cutoff:3.500A) Processing helix chain 'k' and resid 5018 through 5024 Processing helix chain 'k' and resid 5027 through 5044 removed outlier: 3.516A pdb=" N LEU k5031 " --> pdb=" O VAL k5027 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU k5033 " --> pdb=" O PRO k5029 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE k5037 " --> pdb=" O LEU k5033 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL k5043 " --> pdb=" O TRP k5039 " (cutoff:3.500A) Processing helix chain 'l' and resid 5013 through 5037 removed outlier: 3.984A pdb=" N GLY l5020 " --> pdb=" O SER l5016 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU l5025 " --> pdb=" O LEU l5021 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER l5033 " --> pdb=" O LEU l5029 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR l5034 " --> pdb=" O LEU l5030 " (cutoff:3.500A) Processing helix chain 'm' and resid 5006 through 5032 removed outlier: 3.745A pdb=" N ALA m5010 " --> pdb=" O LEU m5006 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR m5011 " --> pdb=" O GLY m5007 " (cutoff:3.500A) Proline residue: m5018 - end of helix removed outlier: 3.647A pdb=" N LEU m5025 " --> pdb=" O PHE m5021 " (cutoff:3.500A) Processing helix chain 't' and resid 5002 through 5023 removed outlier: 3.853A pdb=" N TYR t5006 " --> pdb=" O GLU t5002 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE t5019 " --> pdb=" O ALA t5015 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE t5022 " --> pdb=" O PHE t5018 " (cutoff:3.500A) Processing helix chain 'z' and resid 5002 through 5029 removed outlier: 3.683A pdb=" N VAL z5013 " --> pdb=" O LEU z5009 " (cutoff:3.500A) Proline residue: z5024 - end of helix removed outlier: 3.920A pdb=" N SER z5029 " --> pdb=" O VAL z5025 " (cutoff:3.500A) Processing helix chain 'z' and resid 5032 through 5037 Processing helix chain 'z' and resid 5038 through 5062 removed outlier: 3.854A pdb=" N GLY z5045 " --> pdb=" O PHE z5041 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU z5046 " --> pdb=" O LEU z5042 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA z5049 " --> pdb=" O GLY z5045 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU z5050 " --> pdb=" O LEU z5046 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL z5051 " --> pdb=" O TRP z5047 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU z5052 " --> pdb=" O ILE z5048 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL z5054 " --> pdb=" O LEU z5050 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY z5055 " --> pdb=" O VAL z5051 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL z5056 " --> pdb=" O LEU z5052 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU z5057 " --> pdb=" O VAL z5053 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE z5060 " --> pdb=" O VAL z5056 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 42 removed outlier: 3.558A pdb=" N GLY Y 32 " --> pdb=" O ILE Y 28 " (cutoff:3.500A) Proline residue: Y 33 - end of helix removed outlier: 3.805A pdb=" N ILE Y 36 " --> pdb=" O GLY Y 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 32 through 48 removed outlier: 4.007A pdb=" N ASP n 36 " --> pdb=" O ASN n 32 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER n 43 " --> pdb=" O ALA n 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU n 46 " --> pdb=" O SER n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 77 removed outlier: 3.558A pdb=" N LYS n 67 " --> pdb=" O GLU n 63 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU n 68 " --> pdb=" O ALA n 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN n 69 " --> pdb=" O ARG n 65 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU n 74 " --> pdb=" O ASP n 70 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR n 75 " --> pdb=" O PHE n 71 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG n 77 " --> pdb=" O ALA n 73 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 104 removed outlier: 3.570A pdb=" N MET n 88 " --> pdb=" O LEU n 84 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR n 101 " --> pdb=" O LEU n 97 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER n 102 " --> pdb=" O ALA n 98 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER n 103 " --> pdb=" O GLY n 99 " (cutoff:3.500A) Processing helix chain 'n' and resid 110 through 133 removed outlier: 3.730A pdb=" N ARG n 116 " --> pdb=" O LYS n 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU n 117 " --> pdb=" O LEU n 113 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU n 118 " --> pdb=" O LYS n 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU n 126 " --> pdb=" O LYS n 122 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA n 132 " --> pdb=" O LEU n 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 48 removed outlier: 4.007A pdb=" N ASP N 36 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 77 removed outlier: 3.558A pdb=" N LYS N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN N 69 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR N 75 " --> pdb=" O PHE N 71 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 104 removed outlier: 3.571A pdb=" N MET N 88 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR N 101 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER N 103 " --> pdb=" O GLY N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 133 removed outlier: 3.645A pdb=" N LEU N 117 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU N 118 " --> pdb=" O LYS N 114 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU N 120 " --> pdb=" O ARG N 116 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA N 132 " --> pdb=" O LEU N 128 " (cutoff:3.500A) Processing helix chain 'y' and resid 19 through 29 Processing helix chain 'y' and resid 30 through 43 removed outlier: 3.541A pdb=" N MET y 34 " --> pdb=" O ILE y 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 35 Processing helix chain 'x' and resid 4 through 35 removed outlier: 3.643A pdb=" N PHE x 25 " --> pdb=" O LEU x 21 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 4.583A pdb=" N ASP A 61 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.711A pdb=" N LEU A 174 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.116A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 345 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 341 through 343 Processing sheet with id=AA6, first strand: chain 'a' and resid 5081 through 5082 removed outlier: 3.710A pdb=" N LEU a5174 " --> pdb=" O VAL a5082 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 5336 through 5337 Processing sheet with id=AA8, first strand: chain 'b' and resid 5377 through 5380 removed outlier: 4.117A pdb=" N PHE b5346 " --> pdb=" O LEU b5354 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL b5356 " --> pdb=" O ALA b5344 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N ALA b5344 " --> pdb=" O VAL b5356 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL b5345 " --> pdb=" O SER b5400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 5341 through 5343 1738 hydrogen bonds defined for protein. 5082 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: 6.90 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 12861 1.37 - 1.55: 29030 1.55 - 1.73: 97 1.73 - 1.91: 246 1.91 - 2.08: 288 Bond restraints: 42522 Sorted by residual: bond pdb=" C10 PQ9 A 406 " pdb=" C5 PQ9 A 406 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C10 PQ9 a5407 " pdb=" C5 PQ9 a5407 " ideal model delta sigma weight residual 1.346 1.479 -0.133 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C1A MGE D 409 " pdb=" O1G MGE D 409 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1A MGE b5620 " pdb=" O1G MGE b5620 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C1A MGE d5408 " pdb=" O1G MGE d5408 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.68e+01 ... (remaining 42517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 57195 3.44 - 6.87: 1304 6.87 - 10.31: 211 10.31 - 13.74: 43 13.74 - 17.18: 6 Bond angle restraints: 58759 Sorted by residual: angle pdb=" C ILE y 28 " pdb=" N GLY y 29 " pdb=" CA GLY y 29 " ideal model delta sigma weight residual 121.41 104.23 17.18 1.96e+00 2.60e-01 7.68e+01 angle pdb=" CG1 VAL A 249 " pdb=" CB VAL A 249 " pdb=" CG2 VAL A 249 " ideal model delta sigma weight residual 110.80 94.98 15.82 2.20e+00 2.07e-01 5.17e+01 angle pdb=" N ALA y 20 " pdb=" CA ALA y 20 " pdb=" C ALA y 20 " ideal model delta sigma weight residual 111.14 103.51 7.63 1.08e+00 8.57e-01 4.99e+01 angle pdb=" N ILE y 28 " pdb=" CA ILE y 28 " pdb=" C ILE y 28 " ideal model delta sigma weight residual 110.62 116.91 -6.29 1.02e+00 9.61e-01 3.81e+01 angle pdb=" N ARG A 64 " pdb=" CA ARG A 64 " pdb=" C ARG A 64 " ideal model delta sigma weight residual 110.80 123.94 -13.14 2.13e+00 2.20e-01 3.80e+01 ... (remaining 58754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.90: 21858 34.90 - 69.81: 937 69.81 - 104.71: 164 104.71 - 139.62: 193 139.62 - 174.52: 4 Dihedral angle restraints: 23156 sinusoidal: 10976 harmonic: 12180 Sorted by residual: dihedral pdb=" CA ARG A 64 " pdb=" C ARG A 64 " pdb=" N GLU A 65 " pdb=" CA GLU A 65 " ideal model delta harmonic sigma weight residual 180.00 134.97 45.03 0 5.00e+00 4.00e-02 8.11e+01 dihedral pdb=" CA ILE k5017 " pdb=" C ILE k5017 " pdb=" N PHE k5018 " pdb=" CA PHE k5018 " ideal model delta harmonic sigma weight residual 180.00 136.44 43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ILE K 17 " pdb=" C ILE K 17 " pdb=" N PHE K 18 " pdb=" CA PHE K 18 " ideal model delta harmonic sigma weight residual 180.00 136.50 43.50 0 5.00e+00 4.00e-02 7.57e+01 ... (remaining 23153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 5611 0.147 - 0.294: 164 0.294 - 0.441: 5 0.441 - 0.588: 2 0.588 - 0.736: 1 Chirality restraints: 5783 Sorted by residual: chirality pdb=" CB VAL a5249 " pdb=" CA VAL a5249 " pdb=" CG1 VAL a5249 " pdb=" CG2 VAL a5249 " both_signs ideal model delta sigma weight residual False -2.63 -1.89 -0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB VAL C 410 " pdb=" CA VAL C 410 " pdb=" CG1 VAL C 410 " pdb=" CG2 VAL C 410 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" CA ILE y 28 " pdb=" N ILE y 28 " pdb=" C ILE y 28 " pdb=" CB ILE y 28 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.53 2.00e-01 2.50e+01 7.08e+00 ... (remaining 5780 not shown) Planarity restraints: 7323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " 0.059 2.00e-02 2.50e+03 1.24e-01 1.23e+03 pdb=" ND PHO A 404 " 0.198 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " 0.009 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " 0.024 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " 0.045 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " 0.049 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " 0.074 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " -0.126 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " 0.062 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " -0.036 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " 0.334 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " -0.159 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " 0.056 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " -0.064 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " 0.161 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " -0.026 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " 0.048 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.033 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " -0.254 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " 0.067 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " -0.127 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " -0.256 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " -0.071 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " 0.135 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " -0.001 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " 0.000 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " -0.185 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " 0.065 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " -0.119 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " 0.069 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " 0.035 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO a5405 " -0.059 2.00e-02 2.50e+03 1.24e-01 1.22e+03 pdb=" ND PHO a5405 " -0.198 2.00e-02 2.50e+03 pdb=" C1A PHO a5405 " -0.008 2.00e-02 2.50e+03 pdb=" C1B PHO a5405 " -0.023 2.00e-02 2.50e+03 pdb=" C1C PHO a5405 " -0.045 2.00e-02 2.50e+03 pdb=" C1D PHO a5405 " -0.048 2.00e-02 2.50e+03 pdb=" C2A PHO a5405 " -0.075 2.00e-02 2.50e+03 pdb=" C2B PHO a5405 " 0.125 2.00e-02 2.50e+03 pdb=" C2C PHO a5405 " -0.061 2.00e-02 2.50e+03 pdb=" C2D PHO a5405 " 0.036 2.00e-02 2.50e+03 pdb=" C3A PHO a5405 " -0.333 2.00e-02 2.50e+03 pdb=" C3B PHO a5405 " 0.159 2.00e-02 2.50e+03 pdb=" C3C PHO a5405 " -0.056 2.00e-02 2.50e+03 pdb=" C3D PHO a5405 " 0.064 2.00e-02 2.50e+03 pdb=" C4A PHO a5405 " -0.161 2.00e-02 2.50e+03 pdb=" C4B PHO a5405 " 0.026 2.00e-02 2.50e+03 pdb=" C4C PHO a5405 " -0.048 2.00e-02 2.50e+03 pdb=" C4D PHO a5405 " -0.033 2.00e-02 2.50e+03 pdb=" CAB PHO a5405 " 0.254 2.00e-02 2.50e+03 pdb=" CAC PHO a5405 " -0.067 2.00e-02 2.50e+03 pdb=" CAD PHO a5405 " 0.127 2.00e-02 2.50e+03 pdb=" CBD PHO a5405 " 0.256 2.00e-02 2.50e+03 pdb=" CHA PHO a5405 " 0.071 2.00e-02 2.50e+03 pdb=" CHB PHO a5405 " -0.136 2.00e-02 2.50e+03 pdb=" CHC PHO a5405 " 0.000 2.00e-02 2.50e+03 pdb=" CHD PHO a5405 " -0.001 2.00e-02 2.50e+03 pdb=" CMB PHO a5405 " 0.185 2.00e-02 2.50e+03 pdb=" CMC PHO a5405 " -0.064 2.00e-02 2.50e+03 pdb=" CMD PHO a5405 " 0.119 2.00e-02 2.50e+03 pdb=" NA PHO a5405 " -0.069 2.00e-02 2.50e+03 pdb=" NC PHO a5405 " -0.035 2.00e-02 2.50e+03 pdb=" OBD PHO a5405 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 BCR C 516 " 0.248 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C13 BCR C 516 " -0.197 2.00e-02 2.50e+03 pdb=" C14 BCR C 516 " -0.486 2.00e-02 2.50e+03 pdb=" C15 BCR C 516 " 0.360 2.00e-02 2.50e+03 pdb=" C35 BCR C 516 " 0.075 2.00e-02 2.50e+03 ... (remaining 7320 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 17 1.99 - 2.72: 3099 2.72 - 3.44: 62156 3.44 - 4.17: 99153 4.17 - 4.90: 177166 Nonbonded interactions: 341591 Sorted by model distance: nonbonded pdb=" OE2 GLU m5002 " pdb=" O4' LMT m5102 " model vdw 1.261 3.040 nonbonded pdb=" OD2 ASP k5019 " pdb=" CD GLN y 21 " model vdw 1.491 3.270 nonbonded pdb=" OE1 GLU H 47 " pdb=" CD2 PHE X 10 " model vdw 1.497 3.340 nonbonded pdb=" OD2 ASP k5019 " pdb=" CG GLN y 21 " model vdw 1.561 3.440 nonbonded pdb=" OE2 GLU H 47 " pdb=" CD2 PHE X 10 " model vdw 1.630 3.340 ... (remaining 341586 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 12 through 333 or resid 402 through 403)) selection = (chain 'a' and (resid 5012 through 5333 or resid 5402 through 5403)) } ncs_group { reference = (chain 'B' and (resid 2 through 484 or (resid 485 and (name N or name CA or name \ C or name O or name CB )) or resid 601 through 605 or (resid 606 and (name NB o \ r name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or \ name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CED \ or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name \ CMB or name CMC or name CMD or name NA or name NC or name O1D or name O2D or na \ me OBD or name MG )) or resid 607 through 618)) selection = (chain 'b' and resid 5002 through 5618) } ncs_group { reference = (chain 'C' and (resid 27 through 510 or (resid 511 and (name NB or name ND or na \ me C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2A or \ name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name C3C \ or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or name C \ 5 or name C6 or name CAA or name CAB or name CAC or name CAD or name CBA or name \ CBB or name CBC or name CBD or name CED or name CGA or name CGD or name CHA or \ name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD \ or name NA or name NC or name O1A or name O1D or name O2A or name O2D or name O \ BD or name MG )) or (resid 512 and (name NB or name ND or name C1 or name C1A or \ name C1B or name C1C or name C1D or name C2 or name C2A or name C2B or name C2C \ or name C2D or name C3 or name C3A or name C3B or name C3C or name C3D or name \ C4 or name C4A or name C4B or name C4C or name C4D or name C5 or name CAA or nam \ e CAB or name CAC or name CAD or name CBA or name CBB or name CBC or name CBD or \ name CED or name CGA or name CGD or name CHA or name CHB or name CHC or name CH \ D or name CMA or name CMB or name CMC or name CMD or name NA or name NC or name \ O1A or name O1D or name O2A or name O2D or name OBD or name MG )) or resid 514)) \ selection = (chain 'c' and (resid 5027 through 5512 or resid 5514)) } ncs_group { reference = (chain 'D' and (resid 13 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 402 or (resid 404 and (name NB or \ name ND or name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or \ name C2A or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B \ or name C3C or name C3D or name C4 or name C4A or name C4B or name C4C or name \ C4D or name C5 or name CAA or name CAB or name CAC or name CAD or name CBA or na \ me CBB or name CBC or name CBD or name CED or name CGA or name CGD or name CHA o \ r name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name C \ MD or name NA or name NC or name O1A or name O1D or name O2A or name O2D or name \ OBD or name MG )) or resid 408 through 410)) selection = (chain 'd' and (resid 5013 through 5402 or resid 5404 or resid 5408 through 5410 \ )) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'F' and resid 17 through 101) selection = chain 'f' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = (chain 'K' and resid 12 through 45) selection = (chain 'k' and resid 5012 through 5045) } ncs_group { reference = (chain 'L' and resid 1 through 37) selection = (chain 'l' and resid 5001 through 5037) } ncs_group { reference = (chain 'M' and resid 1 through 33) selection = (chain 'm' and resid 5001 through 5033) } ncs_group { reference = chain 'N' selection = chain 'n' } ncs_group { reference = (chain 'T' and (resid 1 through 30 or resid 102)) selection = (chain 't' and (resid 5001 through 5030 or resid 5102)) } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = (chain 'Y' and resid 18 through 46) selection = chain 'y' } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 5001 through 5062) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.720 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 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 : 0.021 0.895 42594 Z= 1.822 Angle : 1.220 17.176 58759 Z= 0.528 Chirality : 0.062 0.736 5783 Planarity : 0.023 0.307 7323 Dihedral : 22.017 174.524 15372 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.47 % Favored : 91.39 % Rotamer: Outliers : 1.63 % Allowed : 1.69 % Favored : 96.67 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.41 (0.10), residues: 4240 helix: -3.34 (0.07), residues: 2299 sheet: -1.11 (1.01), residues: 20 loop : -2.25 (0.12), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 472 TYR 0.096 0.004 TYR b5258 PHE 0.040 0.003 PHE B 462 TRP 0.055 0.003 TRP A 142 HIS 0.018 0.003 HIS b5343 Details of bonding type rmsd covalent geometry : bond 0.01158 (42522) covalent geometry : angle 1.22025 (58759) hydrogen bonds : bond 0.30252 ( 1738) hydrogen bonds : angle 10.57747 ( 5082) Misc. bond : bond 0.43605 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 991 time to evaluate : 1.248 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8901 (tt) cc_final: 0.8465 (tp) REVERT: A 226 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6376 (tm-30) REVERT: A 269 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8604 (mtm180) REVERT: B 485 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.3742 (tp30) REVERT: C 218 PHE cc_start: 0.7561 (m-80) cc_final: 0.7210 (m-10) REVERT: C 265 ILE cc_start: 0.9252 (mm) cc_final: 0.9050 (tp) REVERT: C 272 LEU cc_start: 0.9644 (tp) cc_final: 0.9413 (tp) REVERT: D 211 CYS cc_start: 0.8999 (t) cc_final: 0.8789 (t) REVERT: D 244 TYR cc_start: 0.8904 (p90) cc_final: 0.8639 (p90) REVERT: E 67 THR cc_start: 0.8023 (m) cc_final: 0.7633 (p) REVERT: I 1 MET cc_start: 0.6292 (mmm) cc_final: 0.5954 (mmp) REVERT: I 5 LYS cc_start: 0.8986 (tttt) cc_final: 0.8550 (tttm) REVERT: I 10 ILE cc_start: 0.9272 (mm) cc_final: 0.8859 (mt) REVERT: K 28 ILE cc_start: 0.8827 (pt) cc_final: 0.8596 (mp) REVERT: L 4 ASN cc_start: 0.8043 (t0) cc_final: 0.7783 (t0) REVERT: L 16 SER cc_start: 0.9029 (m) cc_final: 0.8777 (t) REVERT: M 16 LEU cc_start: 0.9110 (mp) cc_final: 0.8777 (mp) REVERT: Z 59 PHE cc_start: 0.8182 (t80) cc_final: 0.7954 (t80) REVERT: a 5180 PHE cc_start: 0.9190 (m-10) cc_final: 0.8913 (m-10) REVERT: a 5194 MET cc_start: 0.8426 (mmm) cc_final: 0.7994 (mmm) REVERT: a 5261 GLN cc_start: 0.6368 (tt0) cc_final: 0.6146 (pp30) REVERT: a 5319 ASP cc_start: 0.8429 (m-30) cc_final: 0.7867 (t0) REVERT: b 5025 MET cc_start: 0.8651 (tpt) cc_final: 0.8081 (tpt) REVERT: c 5091 HIS cc_start: 0.8367 (m90) cc_final: 0.8159 (m-70) REVERT: c 5230 LEU cc_start: 0.8441 (mt) cc_final: 0.8043 (mp) REVERT: c 5282 MET cc_start: 0.9007 (mtp) cc_final: 0.8539 (mtp) REVERT: c 5288 CYS cc_start: 0.8014 (t) cc_final: 0.7773 (t) REVERT: c 5297 TYR cc_start: 0.7806 (m-80) cc_final: 0.7477 (m-80) REVERT: d 5224 GLN cc_start: 0.8494 (tt0) cc_final: 0.8204 (tt0) REVERT: e 5067 THR cc_start: 0.7566 (m) cc_final: 0.7220 (p) REVERT: m 5015 VAL cc_start: 0.9525 (t) cc_final: 0.9271 (t) REVERT: m 5016 LEU cc_start: 0.8786 (mp) cc_final: 0.8479 (mp) REVERT: Y 43 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7729 (tpp-160) REVERT: y 23 THR cc_start: 0.4391 (OUTLIER) cc_final: 0.4188 (p) REVERT: x 11 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7926 (t80) outliers start: 56 outliers final: 34 residues processed: 1024 average time/residue: 0.2475 time to fit residues: 419.2582 Evaluate side-chains 657 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 619 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain c residue 5410 VAL Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 28 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 42 ARG Chi-restraints excluded: chain Y residue 43 ARG Chi-restraints excluded: chain Y residue 46 LEU Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 38 LEU Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain y residue 41 VAL Chi-restraints excluded: chain y residue 43 ARG Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain X residue 15 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain X residue 29 ILE Chi-restraints excluded: chain X residue 34 ILE Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain x residue 8 LYS Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 15 LEU Chi-restraints excluded: chain x residue 16 SER Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 29 ILE Chi-restraints excluded: chain x residue 34 ILE Chi-restraints excluded: chain x residue 36 LYS Chi-restraints excluded: chain x residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 130 GLN A 322 ASN A 325 ASN B 274 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 338 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 311 GLN C 441 HIS D 61 HIS ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN D 301 GLN E 23 HIS ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN M 4 ASN Z 58 ASN a5087 ASN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5296 ASN a5322 ASN b5053 ASN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5289 GLN b5317 ASN b5338 GLN ** b5343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c5084 GLN c5311 GLN c5382 ASN c5441 HIS d5061 HIS ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d5301 GLN d5334 GLN e5023 HIS ** k5040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l5008 GLN ** m5032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 GLN n 91 GLN n 100 HIS n 119 GLN N 100 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099303 restraints weight = 91515.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102360 restraints weight = 44969.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103048 restraints weight = 29192.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103335 restraints weight = 22421.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103356 restraints weight = 21839.700| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 42594 Z= 0.214 Angle : 0.937 17.574 58759 Z= 0.414 Chirality : 0.050 0.359 5783 Planarity : 0.006 0.064 7323 Dihedral : 23.467 179.774 8267 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 4.44 % Allowed : 10.62 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4240 helix: -0.39 (0.10), residues: 2380 sheet: -1.59 (0.91), residues: 24 loop : -1.69 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 76 TYR 0.030 0.003 TYR m5026 PHE 0.039 0.002 PHE X 10 TRP 0.031 0.002 TRP a5317 HIS 0.011 0.002 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00471 (42522) covalent geometry : angle 0.93739 (58759) hydrogen bonds : bond 0.05917 ( 1738) hydrogen bonds : angle 5.77535 ( 5082) Misc. bond : bond 0.01665 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 815 time to evaluate : 1.330 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: A 112 TYR cc_start: 0.9143 (t80) cc_final: 0.8917 (t80) REVERT: A 167 SER cc_start: 0.8912 (t) cc_final: 0.8633 (p) REVERT: A 226 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6064 (tm-30) REVERT: A 319 ASP cc_start: 0.7722 (m-30) cc_final: 0.7463 (t0) REVERT: A 328 MET cc_start: 0.8105 (mmp) cc_final: 0.7310 (mtm) REVERT: B 37 MET cc_start: 0.9291 (tpp) cc_final: 0.9056 (tpp) REVERT: B 94 GLU cc_start: 0.7095 (mp0) cc_final: 0.6825 (mp0) REVERT: B 188 ASP cc_start: 0.8236 (p0) cc_final: 0.7972 (p0) REVERT: B 256 MET cc_start: 0.8633 (tpp) cc_final: 0.8112 (tpp) REVERT: B 485 GLU cc_start: 0.4434 (OUTLIER) cc_final: 0.3211 (tp30) REVERT: C 218 PHE cc_start: 0.7678 (m-80) cc_final: 0.7428 (m-80) REVERT: C 229 ASN cc_start: 0.7780 (t0) cc_final: 0.7555 (t0) REVERT: C 281 MET cc_start: 0.8799 (ttp) cc_final: 0.8572 (ttm) REVERT: C 308 GLU cc_start: 0.8495 (tt0) cc_final: 0.7724 (mt-10) REVERT: D 19 ASP cc_start: 0.8771 (t70) cc_final: 0.8290 (t0) REVERT: D 85 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8366 (tmm) REVERT: D 129 GLN cc_start: 0.9223 (tt0) cc_final: 0.8816 (tt0) REVERT: F 32 PHE cc_start: 0.8524 (t80) cc_final: 0.8320 (t80) REVERT: F 41 GLN cc_start: 0.8106 (mp10) cc_final: 0.7819 (mp10) REVERT: H 31 MET cc_start: 0.8629 (tmm) cc_final: 0.8334 (tmm) REVERT: I 1 MET cc_start: 0.6749 (mmm) cc_final: 0.6055 (mmt) REVERT: I 10 ILE cc_start: 0.9091 (mm) cc_final: 0.8766 (mt) REVERT: I 21 PHE cc_start: 0.8792 (m-10) cc_final: 0.8509 (m-80) REVERT: M 16 LEU cc_start: 0.9160 (mp) cc_final: 0.8860 (mp) REVERT: T 8 PHE cc_start: 0.8975 (t80) cc_final: 0.8541 (t80) REVERT: T 12 CYS cc_start: 0.8929 (m) cc_final: 0.8626 (m) REVERT: Z 27 TYR cc_start: 0.8590 (m-80) cc_final: 0.8290 (m-80) REVERT: a 5064 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5907 (mtm180) REVERT: a 5112 TYR cc_start: 0.8618 (t80) cc_final: 0.8054 (t80) REVERT: a 5121 LEU cc_start: 0.9046 (tp) cc_final: 0.8727 (tp) REVERT: a 5172 MET cc_start: 0.8985 (ttm) cc_final: 0.8506 (ttm) REVERT: a 5187 GLN cc_start: 0.9412 (tp40) cc_final: 0.8962 (tp-100) REVERT: a 5261 GLN cc_start: 0.6650 (tt0) cc_final: 0.6005 (pp30) REVERT: a 5319 ASP cc_start: 0.8520 (m-30) cc_final: 0.8152 (t0) REVERT: a 5325 ASN cc_start: 0.8534 (m-40) cc_final: 0.8288 (m-40) REVERT: b 5025 MET cc_start: 0.8734 (tpt) cc_final: 0.8270 (tpt) REVERT: b 5037 MET cc_start: 0.9215 (tpp) cc_final: 0.8793 (tpp) REVERT: b 5094 GLU cc_start: 0.7173 (mp0) cc_final: 0.6917 (mp0) REVERT: b 5138 MET cc_start: 0.8636 (ttp) cc_final: 0.8271 (ptm) REVERT: b 5256 MET cc_start: 0.8689 (tpp) cc_final: 0.8435 (tpp) REVERT: c 5389 GLU cc_start: 0.8390 (pt0) cc_final: 0.7788 (pp20) REVERT: c 5395 TYR cc_start: 0.8477 (m-10) cc_final: 0.8204 (m-10) REVERT: d 5080 THR cc_start: 0.8345 (m) cc_final: 0.8054 (p) REVERT: d 5126 MET cc_start: 0.8580 (tpp) cc_final: 0.8326 (tpp) REVERT: d 5129 GLN cc_start: 0.8906 (tt0) cc_final: 0.8610 (tt0) REVERT: d 5210 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8533 (tt) REVERT: e 5067 THR cc_start: 0.7344 (m) cc_final: 0.7080 (p) REVERT: e 5073 LYS cc_start: 0.8355 (tttt) cc_final: 0.8077 (ttpp) REVERT: e 5077 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7491 (mt-10) REVERT: e 5081 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8474 (tm-30) REVERT: i 5001 MET cc_start: 0.6807 (mmt) cc_final: 0.5750 (mmp) REVERT: i 5021 PHE cc_start: 0.8737 (m-10) cc_final: 0.8424 (m-80) REVERT: k 5019 ASP cc_start: 0.7487 (t70) cc_final: 0.7286 (t0) REVERT: l 5004 ASN cc_start: 0.7614 (t0) cc_final: 0.7367 (t0) REVERT: l 5012 LEU cc_start: 0.8475 (tt) cc_final: 0.8107 (tt) REVERT: m 5015 VAL cc_start: 0.9540 (t) cc_final: 0.9090 (t) REVERT: m 5019 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.8962 (p) REVERT: t 5001 MET cc_start: 0.8479 (ttp) cc_final: 0.8256 (tmm) REVERT: t 5008 PHE cc_start: 0.9058 (t80) cc_final: 0.8632 (t80) REVERT: t 5012 CYS cc_start: 0.8780 (m) cc_final: 0.8359 (m) REVERT: Y 42 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7362 (ptp-170) REVERT: Y 43 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8052 (mmp-170) REVERT: n 118 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6682 (tm-30) REVERT: n 119 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6676 (mt0) REVERT: n 120 GLU cc_start: 0.7678 (tt0) cc_final: 0.7229 (tt0) REVERT: N 72 PHE cc_start: 0.8050 (t80) cc_final: 0.7423 (t80) REVERT: y 25 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6174 (mt) REVERT: y 43 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8059 (mmp-170) outliers start: 152 outliers final: 83 residues processed: 886 average time/residue: 0.2321 time to fit residues: 352.0339 Evaluate side-chains 752 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 661 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5064 ARG Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5143 ILE Chi-restraints excluded: chain a residue 5286 THR Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5291 SER Chi-restraints excluded: chain a residue 5300 PHE Chi-restraints excluded: chain a residue 5329 GLU Chi-restraints excluded: chain b residue 5024 LEU Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5214 LEU Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5249 ILE Chi-restraints excluded: chain c residue 5410 VAL Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5138 VAL Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain h residue 5060 VAL Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain k residue 5021 LEU Chi-restraints excluded: chain l residue 5016 SER Chi-restraints excluded: chain m residue 5011 THR Chi-restraints excluded: chain m residue 5013 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5013 ILE Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain z residue 5056 VAL Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 42 ARG Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 119 GLN Chi-restraints excluded: chain n residue 124 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 16 SER Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 139 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 273 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 396 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 234 ASN A 241 GLN B 53 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5108 ASN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5234 ASN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5087 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096830 restraints weight = 91494.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100334 restraints weight = 40515.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102594 restraints weight = 25528.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104014 restraints weight = 19559.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.104670 restraints weight = 16689.233| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 42594 Z= 0.153 Angle : 0.804 15.436 58759 Z= 0.355 Chirality : 0.046 0.338 5783 Planarity : 0.005 0.063 7323 Dihedral : 20.278 177.758 8218 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 4.58 % Allowed : 14.24 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4240 helix: 0.56 (0.10), residues: 2427 sheet: -1.46 (0.86), residues: 24 loop : -1.55 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG n 116 TYR 0.028 0.002 TYR m5026 PHE 0.029 0.002 PHE b5451 TRP 0.044 0.002 TRP a5317 HIS 0.007 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00337 (42522) covalent geometry : angle 0.80443 (58759) hydrogen bonds : bond 0.04869 ( 1738) hydrogen bonds : angle 5.10699 ( 5082) Misc. bond : bond 0.03265 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 769 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.9051 (t80) cc_final: 0.8756 (t80) REVERT: A 167 SER cc_start: 0.9156 (t) cc_final: 0.8828 (p) REVERT: A 226 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6023 (tm-30) REVERT: A 238 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7827 (mmmm) REVERT: A 304 HIS cc_start: 0.7681 (m-70) cc_final: 0.7402 (m-70) REVERT: A 319 ASP cc_start: 0.7790 (m-30) cc_final: 0.7528 (t0) REVERT: A 328 MET cc_start: 0.7971 (mmp) cc_final: 0.7441 (mtm) REVERT: B 37 MET cc_start: 0.9277 (tpp) cc_final: 0.9058 (tpp) REVERT: B 188 ASP cc_start: 0.8307 (p0) cc_final: 0.8102 (p0) REVERT: B 317 ASN cc_start: 0.7952 (t0) cc_final: 0.7356 (t0) REVERT: C 119 LEU cc_start: 0.8570 (mt) cc_final: 0.8130 (mt) REVERT: C 120 ILE cc_start: 0.8914 (mm) cc_final: 0.8326 (pt) REVERT: C 281 MET cc_start: 0.8766 (ttp) cc_final: 0.8529 (ttt) REVERT: C 356 MET cc_start: 0.8963 (tmm) cc_final: 0.8726 (tmm) REVERT: D 19 ASP cc_start: 0.8683 (t70) cc_final: 0.8366 (t0) REVERT: D 85 MET cc_start: 0.8825 (tmm) cc_final: 0.8576 (tmm) REVERT: D 126 MET cc_start: 0.8351 (tpp) cc_final: 0.7993 (tpp) REVERT: D 129 GLN cc_start: 0.9108 (tt0) cc_final: 0.8593 (tt0) REVERT: D 160 TYR cc_start: 0.9230 (t80) cc_final: 0.8893 (t80) REVERT: D 312 GLU cc_start: 0.7983 (tp30) cc_final: 0.7687 (tp30) REVERT: I 1 MET cc_start: 0.6863 (mmm) cc_final: 0.6231 (mmp) REVERT: I 21 PHE cc_start: 0.8742 (m-10) cc_final: 0.8457 (m-80) REVERT: L 4 ASN cc_start: 0.7621 (t0) cc_final: 0.7001 (t0) REVERT: M 5 GLN cc_start: 0.7151 (mp10) cc_final: 0.6809 (mp10) REVERT: T 8 PHE cc_start: 0.8904 (t80) cc_final: 0.8375 (t80) REVERT: T 12 CYS cc_start: 0.8865 (m) cc_final: 0.8505 (m) REVERT: T 18 PHE cc_start: 0.9186 (t80) cc_final: 0.8966 (t80) REVERT: Z 27 TYR cc_start: 0.8643 (m-80) cc_final: 0.8396 (m-80) REVERT: a 5064 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5777 (mtm180) REVERT: a 5112 TYR cc_start: 0.8674 (t80) cc_final: 0.8080 (t80) REVERT: a 5121 LEU cc_start: 0.8954 (tp) cc_final: 0.8608 (tp) REVERT: a 5172 MET cc_start: 0.9028 (ttm) cc_final: 0.8556 (ttt) REVERT: a 5187 GLN cc_start: 0.9446 (tp40) cc_final: 0.8877 (tp-100) REVERT: a 5261 GLN cc_start: 0.6622 (tt0) cc_final: 0.6058 (pp30) REVERT: a 5319 ASP cc_start: 0.8418 (m-30) cc_final: 0.8019 (t0) REVERT: a 5325 ASN cc_start: 0.8699 (m-40) cc_final: 0.8343 (m-40) REVERT: b 5025 MET cc_start: 0.8674 (tpt) cc_final: 0.8331 (tpt) REVERT: b 5138 MET cc_start: 0.8521 (ttp) cc_final: 0.8264 (ptm) REVERT: b 5256 MET cc_start: 0.8592 (tpp) cc_final: 0.8274 (tpp) REVERT: c 5187 ASP cc_start: 0.7593 (t0) cc_final: 0.7361 (t0) REVERT: c 5282 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: c 5293 ASN cc_start: 0.8813 (t0) cc_final: 0.8605 (t0) REVERT: c 5302 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: c 5389 GLU cc_start: 0.8509 (pt0) cc_final: 0.7925 (pp20) REVERT: d 5085 MET cc_start: 0.8870 (tmm) cc_final: 0.8650 (tmm) REVERT: d 5126 MET cc_start: 0.8532 (tpp) cc_final: 0.8188 (tpp) REVERT: d 5129 GLN cc_start: 0.8853 (tt0) cc_final: 0.8127 (tt0) REVERT: d 5160 TYR cc_start: 0.9262 (t80) cc_final: 0.8873 (t80) REVERT: d 5210 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8558 (tt) REVERT: d 5244 TYR cc_start: 0.8990 (p90) cc_final: 0.8696 (p90) REVERT: d 5297 ASP cc_start: 0.7351 (t0) cc_final: 0.7124 (t0) REVERT: d 5333 ASP cc_start: 0.7936 (t70) cc_final: 0.7498 (t0) REVERT: d 5334 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8585 (mm110) REVERT: i 5001 MET cc_start: 0.6419 (mmt) cc_final: 0.5472 (mmp) REVERT: i 5021 PHE cc_start: 0.8710 (m-10) cc_final: 0.8392 (m-80) REVERT: k 5019 ASP cc_start: 0.7686 (t70) cc_final: 0.7464 (t0) REVERT: l 5004 ASN cc_start: 0.7398 (t0) cc_final: 0.6951 (t0) REVERT: l 5011 GLU cc_start: 0.8328 (pt0) cc_final: 0.8125 (pm20) REVERT: m 5015 VAL cc_start: 0.9583 (t) cc_final: 0.9102 (t) REVERT: m 5019 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8845 (p) REVERT: t 5008 PHE cc_start: 0.9068 (t80) cc_final: 0.8624 (t80) REVERT: t 5012 CYS cc_start: 0.8807 (m) cc_final: 0.8363 (m) REVERT: Y 43 ARG cc_start: 0.8494 (mtp-110) cc_final: 0.8046 (mmp-170) REVERT: n 118 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6866 (tm-30) REVERT: n 119 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6448 (mt0) REVERT: n 120 GLU cc_start: 0.7825 (tt0) cc_final: 0.7336 (tt0) REVERT: N 90 MET cc_start: 0.9133 (tpt) cc_final: 0.8882 (tpt) REVERT: N 91 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8681 (tm-30) REVERT: N 118 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6481 (tm-30) REVERT: y 43 ARG cc_start: 0.8813 (mtp85) cc_final: 0.8081 (tpm170) outliers start: 157 outliers final: 83 residues processed: 857 average time/residue: 0.2331 time to fit residues: 343.7784 Evaluate side-chains 752 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 663 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain T residue 17 PHE Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5064 ARG Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5317 TRP Chi-restraints excluded: chain a residue 5329 GLU Chi-restraints excluded: chain b residue 5214 LEU Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5410 THR Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5282 MET Chi-restraints excluded: chain c residue 5302 TYR Chi-restraints excluded: chain c residue 5396 MET Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5065 SER Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5138 VAL Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5277 THR Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain l residue 5016 SER Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5013 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain t residue 5017 PHE Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 30 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 36 ASP Chi-restraints excluded: chain n residue 119 GLN Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 307 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 251 optimal weight: 0.0470 chunk 369 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 351 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 273 optimal weight: 9.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 241 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 91 HIS ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 4 ASN M 32 GLN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5318 ASN c5091 HIS ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c5382 ASN ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e5074 GLN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098176 restraints weight = 90908.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101617 restraints weight = 39930.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103843 restraints weight = 25001.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105165 restraints weight = 19072.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 77)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106046 restraints weight = 16357.147| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.297 42594 Z= 0.141 Angle : 0.763 13.023 58759 Z= 0.337 Chirality : 0.045 0.339 5783 Planarity : 0.005 0.065 7323 Dihedral : 18.541 173.050 8208 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 4.03 % Allowed : 16.46 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4240 helix: 0.85 (0.10), residues: 2439 sheet: -1.17 (0.93), residues: 24 loop : -1.45 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.029 0.002 TYR M 26 PHE 0.025 0.002 PHE C 218 TRP 0.038 0.001 TRP a5317 HIS 0.010 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00312 (42522) covalent geometry : angle 0.76340 (58759) hydrogen bonds : bond 0.04398 ( 1738) hydrogen bonds : angle 4.82405 ( 5082) Misc. bond : bond 0.04033 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 748 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.9043 (t80) cc_final: 0.8786 (t80) REVERT: A 167 SER cc_start: 0.9141 (t) cc_final: 0.8681 (p) REVERT: A 187 GLN cc_start: 0.9410 (tp-100) cc_final: 0.9101 (tp-100) REVERT: A 319 ASP cc_start: 0.7888 (m-30) cc_final: 0.7648 (t0) REVERT: A 328 MET cc_start: 0.7794 (mmp) cc_final: 0.7436 (mtm) REVERT: B 15 ASP cc_start: 0.7619 (m-30) cc_final: 0.7409 (p0) REVERT: B 317 ASN cc_start: 0.8248 (t0) cc_final: 0.7559 (t0) REVERT: B 485 GLU cc_start: 0.4803 (OUTLIER) cc_final: 0.3002 (tp30) REVERT: C 119 LEU cc_start: 0.8711 (mt) cc_final: 0.8269 (mt) REVERT: C 187 ASP cc_start: 0.8632 (t0) cc_final: 0.8292 (t0) REVERT: C 302 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: C 356 MET cc_start: 0.9075 (tmm) cc_final: 0.8766 (tmm) REVERT: D 19 ASP cc_start: 0.8580 (t70) cc_final: 0.8275 (t0) REVERT: D 85 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8307 (tmm) REVERT: D 160 TYR cc_start: 0.9231 (t80) cc_final: 0.8994 (t80) REVERT: D 296 TYR cc_start: 0.8049 (t80) cc_final: 0.7451 (t80) REVERT: D 312 GLU cc_start: 0.8220 (tp30) cc_final: 0.7927 (tp30) REVERT: E 69 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.6635 (ttm110) REVERT: H 47 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7438 (mt-10) REVERT: I 1 MET cc_start: 0.6765 (mmm) cc_final: 0.6152 (mmp) REVERT: I 17 LEU cc_start: 0.8782 (tp) cc_final: 0.8424 (mm) REVERT: I 21 PHE cc_start: 0.8631 (m-10) cc_final: 0.8383 (m-80) REVERT: K 19 ASP cc_start: 0.8159 (t70) cc_final: 0.7938 (t0) REVERT: M 15 VAL cc_start: 0.9556 (OUTLIER) cc_final: 0.9299 (t) REVERT: M 19 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8859 (p) REVERT: T 6 TYR cc_start: 0.8285 (m-80) cc_final: 0.8065 (m-80) REVERT: T 8 PHE cc_start: 0.8879 (t80) cc_final: 0.8489 (t80) REVERT: T 12 CYS cc_start: 0.8855 (m) cc_final: 0.8563 (m) REVERT: Z 27 TYR cc_start: 0.8768 (m-80) cc_final: 0.8548 (m-80) REVERT: a 5064 ARG cc_start: 0.6441 (mmm160) cc_final: 0.5799 (mtm180) REVERT: a 5103 ASP cc_start: 0.8227 (t70) cc_final: 0.7979 (t70) REVERT: a 5112 TYR cc_start: 0.8705 (t80) cc_final: 0.8129 (t80) REVERT: a 5121 LEU cc_start: 0.8925 (tp) cc_final: 0.8622 (tp) REVERT: a 5170 ASP cc_start: 0.8488 (m-30) cc_final: 0.8262 (m-30) REVERT: a 5172 MET cc_start: 0.9051 (ttm) cc_final: 0.8588 (ttt) REVERT: a 5181 ASN cc_start: 0.9145 (t0) cc_final: 0.8929 (t0) REVERT: a 5187 GLN cc_start: 0.9486 (tp40) cc_final: 0.8981 (tp-100) REVERT: a 5199 GLN cc_start: 0.9194 (mt0) cc_final: 0.8849 (mt0) REVERT: a 5214 MET cc_start: 0.8202 (tpp) cc_final: 0.7951 (mmt) REVERT: a 5261 GLN cc_start: 0.6503 (tt0) cc_final: 0.5988 (pp30) REVERT: a 5319 ASP cc_start: 0.8389 (m-30) cc_final: 0.7981 (t0) REVERT: a 5325 ASN cc_start: 0.8608 (m-40) cc_final: 0.8319 (m-40) REVERT: b 5025 MET cc_start: 0.8737 (tpt) cc_final: 0.8414 (tpt) REVERT: b 5066 MET cc_start: 0.7949 (mtt) cc_final: 0.7665 (mtp) REVERT: b 5256 MET cc_start: 0.8652 (tpp) cc_final: 0.8384 (tpp) REVERT: b 5317 ASN cc_start: 0.8147 (t0) cc_final: 0.7521 (t0) REVERT: c 5059 LEU cc_start: 0.9292 (mt) cc_final: 0.8970 (tt) REVERT: c 5187 ASP cc_start: 0.7188 (t0) cc_final: 0.6816 (t0) REVERT: c 5282 MET cc_start: 0.8809 (mtm) cc_final: 0.8151 (mtp) REVERT: c 5302 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: c 5389 GLU cc_start: 0.8609 (pt0) cc_final: 0.7960 (pp20) REVERT: d 5085 MET cc_start: 0.8848 (tmm) cc_final: 0.8538 (tmm) REVERT: d 5126 MET cc_start: 0.8460 (tpp) cc_final: 0.8103 (tpp) REVERT: d 5129 GLN cc_start: 0.8883 (tt0) cc_final: 0.8495 (tt0) REVERT: d 5160 TYR cc_start: 0.9279 (t80) cc_final: 0.8915 (t80) REVERT: d 5210 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8409 (tt) REVERT: d 5244 TYR cc_start: 0.8882 (p90) cc_final: 0.8489 (p90) REVERT: d 5295 SER cc_start: 0.9018 (t) cc_final: 0.8472 (p) REVERT: d 5333 ASP cc_start: 0.7873 (t70) cc_final: 0.7217 (t0) REVERT: d 5334 GLN cc_start: 0.8904 (mm110) cc_final: 0.8379 (mm-40) REVERT: e 5082 GLN cc_start: 0.7727 (mm110) cc_final: 0.6999 (pt0) REVERT: f 5041 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7157 (tm-30) REVERT: i 5001 MET cc_start: 0.6346 (mmt) cc_final: 0.5530 (mmp) REVERT: l 5024 ILE cc_start: 0.9417 (mm) cc_final: 0.9162 (tp) REVERT: t 5001 MET cc_start: 0.8188 (ttp) cc_final: 0.7923 (ttp) REVERT: t 5006 TYR cc_start: 0.8267 (m-80) cc_final: 0.7901 (m-80) REVERT: t 5008 PHE cc_start: 0.9059 (t80) cc_final: 0.8647 (t80) REVERT: t 5012 CYS cc_start: 0.8961 (m) cc_final: 0.8583 (m) REVERT: t 5026 PRO cc_start: 0.8607 (Cg_exo) cc_final: 0.8364 (Cg_endo) REVERT: z 5039 LEU cc_start: 0.8832 (tp) cc_final: 0.8383 (mt) REVERT: Y 43 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.8076 (mmp-170) REVERT: n 118 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7545 (tm-30) REVERT: n 119 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6407 (mt0) REVERT: n 120 GLU cc_start: 0.7858 (tt0) cc_final: 0.6948 (tt0) REVERT: N 91 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8558 (tm-30) REVERT: N 95 ASN cc_start: 0.8431 (p0) cc_final: 0.8055 (p0) REVERT: N 118 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6860 (tm-30) REVERT: y 25 ILE cc_start: 0.6445 (OUTLIER) cc_final: 0.6000 (mt) REVERT: y 43 ARG cc_start: 0.8830 (mtp85) cc_final: 0.8122 (mmp-170) outliers start: 138 outliers final: 85 residues processed: 828 average time/residue: 0.2217 time to fit residues: 316.9600 Evaluate side-chains 772 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 678 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 302 TYR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5120 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5145 VAL Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5188 THR Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5302 TYR Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5013 ASN Chi-restraints excluded: chain l residue 5016 SER Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain t residue 5017 PHE Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain z residue 5050 LEU Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 119 GLN Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 397 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 249 optimal weight: 0.5980 chunk 358 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 88 optimal weight: 0.0370 chunk 350 optimal weight: 8.9990 chunk 256 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 overall best weight: 2.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 130 GLN ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 118 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN D 268 HIS ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c5382 ASN ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e5074 GLN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093522 restraints weight = 91850.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096944 restraints weight = 41191.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099150 restraints weight = 26266.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100345 restraints weight = 20246.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101197 restraints weight = 17539.344| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 42594 Z= 0.218 Angle : 0.781 13.991 58759 Z= 0.347 Chirality : 0.046 0.417 5783 Planarity : 0.005 0.060 7323 Dihedral : 17.735 171.835 8206 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 5.14 % Allowed : 18.18 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4240 helix: 0.89 (0.10), residues: 2451 sheet: -0.81 (1.00), residues: 24 loop : -1.35 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 472 TYR 0.036 0.002 TYR M 26 PHE 0.025 0.002 PHE E 31 TRP 0.033 0.002 TRP c5365 HIS 0.010 0.001 HIS b5201 Details of bonding type rmsd covalent geometry : bond 0.00485 (42522) covalent geometry : angle 0.78096 (58759) hydrogen bonds : bond 0.04438 ( 1738) hydrogen bonds : angle 4.76807 ( 5082) Misc. bond : bond 0.02477 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 701 time to evaluate : 1.267 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: A 89 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 112 TYR cc_start: 0.9104 (t80) cc_final: 0.8802 (t80) REVERT: A 167 SER cc_start: 0.9186 (t) cc_final: 0.8756 (p) REVERT: A 187 GLN cc_start: 0.9241 (tp-100) cc_final: 0.8983 (tp-100) REVERT: A 319 ASP cc_start: 0.8057 (m-30) cc_final: 0.7750 (t0) REVERT: B 15 ASP cc_start: 0.7734 (m-30) cc_final: 0.7526 (p0) REVERT: B 485 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.3140 (tp30) REVERT: C 119 LEU cc_start: 0.8831 (mt) cc_final: 0.8456 (mt) REVERT: C 313 GLN cc_start: 0.8346 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 356 MET cc_start: 0.9144 (tmm) cc_final: 0.8845 (tmm) REVERT: D 19 ASP cc_start: 0.8695 (t70) cc_final: 0.8420 (t70) REVERT: D 85 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8328 (tmm) REVERT: D 126 MET cc_start: 0.8341 (tpp) cc_final: 0.8049 (tpp) REVERT: D 129 GLN cc_start: 0.9020 (mt0) cc_final: 0.8678 (tt0) REVERT: D 160 TYR cc_start: 0.9270 (t80) cc_final: 0.8981 (t80) REVERT: D 295 SER cc_start: 0.8816 (t) cc_final: 0.8350 (p) REVERT: E 69 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7204 (ttm110) REVERT: E 71 GLU cc_start: 0.7986 (mp0) cc_final: 0.7648 (mp0) REVERT: E 73 LYS cc_start: 0.8002 (tttt) cc_final: 0.7570 (ttpp) REVERT: E 82 GLN cc_start: 0.7519 (mt0) cc_final: 0.7227 (pt0) REVERT: F 41 GLN cc_start: 0.7931 (mp10) cc_final: 0.7588 (mp10) REVERT: H 47 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7367 (mt-10) REVERT: I 1 MET cc_start: 0.6849 (mmm) cc_final: 0.6372 (mmp) REVERT: I 21 PHE cc_start: 0.8675 (m-10) cc_final: 0.8382 (m-80) REVERT: L 8 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8530 (mm-40) REVERT: T 8 PHE cc_start: 0.8848 (t80) cc_final: 0.8311 (t80) REVERT: T 12 CYS cc_start: 0.8896 (m) cc_final: 0.8547 (m) REVERT: Z 19 MET cc_start: 0.8535 (tmm) cc_final: 0.8269 (tmm) REVERT: Z 58 ASN cc_start: 0.5535 (OUTLIER) cc_final: 0.5282 (m110) REVERT: a 5064 ARG cc_start: 0.6477 (mmm160) cc_final: 0.5959 (mtm180) REVERT: a 5103 ASP cc_start: 0.8327 (t70) cc_final: 0.8054 (t70) REVERT: a 5112 TYR cc_start: 0.8873 (t80) cc_final: 0.8273 (t80) REVERT: a 5121 LEU cc_start: 0.8963 (tp) cc_final: 0.8589 (tp) REVERT: a 5144 CYS cc_start: 0.8155 (p) cc_final: 0.7947 (p) REVERT: a 5170 ASP cc_start: 0.8568 (m-30) cc_final: 0.8362 (m-30) REVERT: a 5172 MET cc_start: 0.9121 (ttm) cc_final: 0.8705 (ttm) REVERT: a 5193 LEU cc_start: 0.9453 (mt) cc_final: 0.9094 (mt) REVERT: a 5261 GLN cc_start: 0.6413 (tt0) cc_final: 0.6117 (pp30) REVERT: a 5319 ASP cc_start: 0.8515 (m-30) cc_final: 0.8051 (t0) REVERT: b 5015 ASP cc_start: 0.7801 (m-30) cc_final: 0.7258 (p0) REVERT: b 5025 MET cc_start: 0.8774 (tpt) cc_final: 0.8496 (tpt) REVERT: c 5187 ASP cc_start: 0.7384 (t0) cc_final: 0.7043 (t0) REVERT: c 5302 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: d 5085 MET cc_start: 0.8855 (tmm) cc_final: 0.8525 (tmm) REVERT: d 5126 MET cc_start: 0.8353 (tpp) cc_final: 0.8096 (tpp) REVERT: d 5129 GLN cc_start: 0.8960 (tt0) cc_final: 0.8706 (mt0) REVERT: d 5160 TYR cc_start: 0.9315 (t80) cc_final: 0.8950 (t80) REVERT: d 5164 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8672 (mm-40) REVERT: d 5173 PHE cc_start: 0.9073 (m-10) cc_final: 0.8701 (m-80) REVERT: d 5210 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8567 (tt) REVERT: d 5244 TYR cc_start: 0.8955 (p90) cc_final: 0.8575 (p90) REVERT: d 5295 SER cc_start: 0.9017 (t) cc_final: 0.8594 (p) REVERT: d 5333 ASP cc_start: 0.7890 (t70) cc_final: 0.7241 (t0) REVERT: d 5334 GLN cc_start: 0.8939 (mm110) cc_final: 0.8425 (mm110) REVERT: e 5082 GLN cc_start: 0.7701 (mm110) cc_final: 0.7257 (pt0) REVERT: f 5041 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7343 (tm-30) REVERT: i 5001 MET cc_start: 0.6415 (mmt) cc_final: 0.5693 (mmp) REVERT: l 5021 LEU cc_start: 0.9315 (mt) cc_final: 0.9058 (mt) REVERT: l 5024 ILE cc_start: 0.9453 (mm) cc_final: 0.9175 (tp) REVERT: m 5019 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8809 (p) REVERT: t 5008 PHE cc_start: 0.9087 (t80) cc_final: 0.8671 (t80) REVERT: t 5012 CYS cc_start: 0.8934 (m) cc_final: 0.8631 (m) REVERT: t 5018 PHE cc_start: 0.9197 (t80) cc_final: 0.8952 (t80) REVERT: z 5001 MET cc_start: 0.7585 (tpp) cc_final: 0.6528 (ttp) REVERT: z 5039 LEU cc_start: 0.8866 (tp) cc_final: 0.8518 (mt) REVERT: z 5053 VAL cc_start: 0.9311 (p) cc_final: 0.8904 (p) REVERT: Y 43 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8086 (mmp-170) REVERT: n 118 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7574 (tm-30) REVERT: n 119 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6166 (mt0) REVERT: n 120 GLU cc_start: 0.7826 (tt0) cc_final: 0.6917 (tt0) REVERT: N 66 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8300 (mmmt) REVERT: N 87 PHE cc_start: 0.7207 (t80) cc_final: 0.6944 (t80) REVERT: N 91 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8342 (tm-30) REVERT: N 95 ASN cc_start: 0.8403 (p0) cc_final: 0.7824 (p0) REVERT: N 118 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7315 (tm-30) REVERT: y 25 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5739 (mt) REVERT: y 43 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8052 (mmp-170) outliers start: 176 outliers final: 121 residues processed: 811 average time/residue: 0.2176 time to fit residues: 305.2070 Evaluate side-chains 778 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 648 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 58 ASN Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5120 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5145 VAL Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5290 ILE Chi-restraints excluded: chain a residue 5329 GLU Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5365 SER Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5410 THR Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5060 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5302 TYR Chi-restraints excluded: chain c residue 5410 VAL Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5050 THR Chi-restraints excluded: chain d residue 5065 SER Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5281 MET Chi-restraints excluded: chain e residue 5025 ILE Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain f residue 5023 VAL Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5012 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5016 SER Chi-restraints excluded: chain m residue 5009 ILE Chi-restraints excluded: chain m residue 5011 THR Chi-restraints excluded: chain m residue 5013 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain z residue 5004 LEU Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain z residue 5050 LEU Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 119 GLN Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 16 SER Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 42 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 143 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 345 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 HIS C 118 HIS C 229 ASN D 61 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN E 74 GLN L 4 ASN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b5281 GLN c5091 HIS ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5087 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d5129 GLN ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e5074 GLN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 91 GLN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.123813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097663 restraints weight = 91031.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101181 restraints weight = 40384.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103430 restraints weight = 25505.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104578 restraints weight = 19582.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105628 restraints weight = 17058.117| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 42594 Z= 0.131 Angle : 0.720 12.550 58759 Z= 0.320 Chirality : 0.044 0.388 5783 Planarity : 0.005 0.058 7323 Dihedral : 16.983 171.552 8204 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 4.17 % Allowed : 19.59 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.08 (0.13), residues: 4240 helix: 1.04 (0.10), residues: 2451 sheet: -0.53 (1.10), residues: 24 loop : -1.36 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c5362 TYR 0.030 0.002 TYR M 26 PHE 0.029 0.001 PHE t5010 TRP 0.020 0.001 TRP a5317 HIS 0.005 0.001 HIS d5336 Details of bonding type rmsd covalent geometry : bond 0.00290 (42522) covalent geometry : angle 0.71962 (58759) hydrogen bonds : bond 0.04060 ( 1738) hydrogen bonds : angle 4.56587 ( 5082) Misc. bond : bond 0.02151 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 735 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8971 (t80) cc_final: 0.8685 (t80) REVERT: A 167 SER cc_start: 0.9173 (t) cc_final: 0.8675 (p) REVERT: A 187 GLN cc_start: 0.9261 (tp-100) cc_final: 0.9042 (tp-100) REVERT: A 319 ASP cc_start: 0.8021 (m-30) cc_final: 0.7696 (t0) REVERT: B 15 ASP cc_start: 0.7633 (m-30) cc_final: 0.7424 (p0) REVERT: B 145 LEU cc_start: 0.9379 (tt) cc_final: 0.9149 (mt) REVERT: B 256 MET cc_start: 0.8579 (tpp) cc_final: 0.8082 (tpp) REVERT: B 485 GLU cc_start: 0.5007 (OUTLIER) cc_final: 0.3213 (tp30) REVERT: C 95 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8827 (tp) REVERT: C 119 LEU cc_start: 0.8779 (mt) cc_final: 0.8406 (mt) REVERT: C 243 ILE cc_start: 0.9205 (mt) cc_final: 0.9002 (tt) REVERT: C 313 GLN cc_start: 0.8425 (tt0) cc_final: 0.7946 (tm-30) REVERT: C 356 MET cc_start: 0.9147 (tmm) cc_final: 0.8795 (tmm) REVERT: D 19 ASP cc_start: 0.8538 (t70) cc_final: 0.8205 (t0) REVERT: D 85 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8167 (tmm) REVERT: D 126 MET cc_start: 0.8274 (tpp) cc_final: 0.7920 (tpp) REVERT: D 160 TYR cc_start: 0.9203 (t80) cc_final: 0.8893 (t80) REVERT: D 273 PHE cc_start: 0.8838 (t80) cc_final: 0.8562 (t80) REVERT: D 295 SER cc_start: 0.8899 (t) cc_final: 0.8529 (p) REVERT: D 302 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7830 (pp20) REVERT: E 56 TYR cc_start: 0.7315 (m-80) cc_final: 0.6823 (m-80) REVERT: E 69 ARG cc_start: 0.7296 (ttp-110) cc_final: 0.7008 (ttm110) REVERT: E 74 GLN cc_start: 0.9204 (mt0) cc_final: 0.8889 (mt0) REVERT: E 82 GLN cc_start: 0.7525 (mt0) cc_final: 0.7225 (pt0) REVERT: H 47 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7413 (mt-10) REVERT: I 1 MET cc_start: 0.6916 (mmm) cc_final: 0.6465 (mmp) REVERT: I 17 LEU cc_start: 0.8980 (tp) cc_final: 0.8686 (mm) REVERT: L 8 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8543 (mm-40) REVERT: M 15 VAL cc_start: 0.9583 (t) cc_final: 0.9198 (t) REVERT: M 19 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8821 (p) REVERT: T 8 PHE cc_start: 0.8830 (t80) cc_final: 0.8363 (t80) REVERT: T 12 CYS cc_start: 0.8918 (m) cc_final: 0.8602 (m) REVERT: a 5064 ARG cc_start: 0.6396 (mmm160) cc_final: 0.5783 (mtm180) REVERT: a 5098 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6898 (tm-30) REVERT: a 5103 ASP cc_start: 0.8256 (t70) cc_final: 0.7949 (t70) REVERT: a 5112 TYR cc_start: 0.8765 (t80) cc_final: 0.8152 (t80) REVERT: a 5172 MET cc_start: 0.9103 (ttm) cc_final: 0.8618 (ttt) REVERT: a 5183 MET cc_start: 0.8834 (mmt) cc_final: 0.8287 (mmt) REVERT: a 5187 GLN cc_start: 0.9410 (tp40) cc_final: 0.9193 (tp-100) REVERT: a 5199 GLN cc_start: 0.9187 (mt0) cc_final: 0.8889 (mt0) REVERT: a 5214 MET cc_start: 0.8204 (tpp) cc_final: 0.7794 (mmt) REVERT: a 5261 GLN cc_start: 0.6456 (tt0) cc_final: 0.6190 (pp30) REVERT: b 5015 ASP cc_start: 0.7671 (m-30) cc_final: 0.7275 (p0) REVERT: b 5025 MET cc_start: 0.8712 (tpt) cc_final: 0.8438 (tpt) REVERT: b 5256 MET cc_start: 0.8638 (tpp) cc_final: 0.8347 (tpp) REVERT: c 5059 LEU cc_start: 0.9263 (mt) cc_final: 0.8971 (tt) REVERT: c 5095 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8475 (tp) REVERT: c 5187 ASP cc_start: 0.7125 (t0) cc_final: 0.6656 (t0) REVERT: c 5230 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8146 (mp) REVERT: c 5282 MET cc_start: 0.8791 (mtm) cc_final: 0.7969 (mtm) REVERT: d 5085 MET cc_start: 0.8743 (tmm) cc_final: 0.8301 (tmm) REVERT: d 5126 MET cc_start: 0.8316 (tpp) cc_final: 0.8001 (tpp) REVERT: d 5129 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8591 (mt0) REVERT: d 5160 TYR cc_start: 0.9254 (t80) cc_final: 0.8918 (t80) REVERT: d 5164 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8603 (mm-40) REVERT: d 5210 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8460 (tt) REVERT: d 5244 TYR cc_start: 0.8758 (p90) cc_final: 0.8419 (p90) REVERT: d 5295 SER cc_start: 0.8995 (t) cc_final: 0.8693 (p) REVERT: d 5333 ASP cc_start: 0.7757 (t70) cc_final: 0.6771 (t0) REVERT: d 5334 GLN cc_start: 0.8920 (mm110) cc_final: 0.8046 (mm110) REVERT: e 5077 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7815 (mt-10) REVERT: e 5082 GLN cc_start: 0.7634 (mm110) cc_final: 0.6986 (pt0) REVERT: f 5041 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7358 (tm-30) REVERT: i 5001 MET cc_start: 0.6403 (mmt) cc_final: 0.5735 (mmp) REVERT: i 5002 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6880 (tm-30) REVERT: k 5038 VAL cc_start: 0.9352 (t) cc_final: 0.9136 (p) REVERT: l 5021 LEU cc_start: 0.9279 (mt) cc_final: 0.9067 (mt) REVERT: m 5019 SER cc_start: 0.9086 (OUTLIER) cc_final: 0.8710 (p) REVERT: t 5006 TYR cc_start: 0.8427 (m-80) cc_final: 0.8122 (m-80) REVERT: t 5008 PHE cc_start: 0.8988 (t80) cc_final: 0.8566 (t80) REVERT: t 5012 CYS cc_start: 0.8947 (m) cc_final: 0.8635 (m) REVERT: t 5018 PHE cc_start: 0.9167 (t80) cc_final: 0.8916 (t80) REVERT: z 5001 MET cc_start: 0.7071 (tpp) cc_final: 0.6334 (ttp) REVERT: z 5005 PHE cc_start: 0.7832 (t80) cc_final: 0.7345 (t80) REVERT: z 5039 LEU cc_start: 0.8853 (tp) cc_final: 0.8439 (mt) REVERT: Y 43 ARG cc_start: 0.8454 (mtp-110) cc_final: 0.8060 (mmp-170) REVERT: n 118 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7462 (tm-30) REVERT: n 119 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: n 120 GLU cc_start: 0.7788 (tt0) cc_final: 0.7162 (tt0) REVERT: N 91 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8476 (tm-30) REVERT: N 95 ASN cc_start: 0.8432 (p0) cc_final: 0.7850 (p0) REVERT: y 25 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5900 (mt) REVERT: y 43 ARG cc_start: 0.8854 (mtp85) cc_final: 0.8061 (mmp-170) outliers start: 143 outliers final: 91 residues processed: 820 average time/residue: 0.2186 time to fit residues: 310.0901 Evaluate side-chains 774 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 671 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 37 PHE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5047 CYS Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5060 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5230 LEU Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5436 PHE Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain c residue 5472 LEU Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5129 GLN Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5281 MET Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5001 MET Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain t residue 5017 PHE Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 119 GLN Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 36 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 47 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 328 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 295 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 251 optimal weight: 0.0170 overall best weight: 2.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 281 GLN C 118 HIS ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN M 32 GLN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c5091 HIS ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e5074 GLN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 91 GLN n 95 ASN n 119 GLN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095578 restraints weight = 91683.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.097320 restraints weight = 63621.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099452 restraints weight = 35438.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099001 restraints weight = 27257.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099292 restraints weight = 25592.944| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 42594 Z= 0.204 Angle : 0.750 13.347 58759 Z= 0.335 Chirality : 0.045 0.395 5783 Planarity : 0.005 0.055 7323 Dihedral : 16.897 173.097 8202 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 4.70 % Allowed : 20.34 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.17 (0.13), residues: 4240 helix: 1.09 (0.10), residues: 2451 sheet: -0.41 (1.12), residues: 24 loop : -1.29 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l5007 TYR 0.016 0.002 TYR t5006 PHE 0.030 0.002 PHE t5010 TRP 0.019 0.001 TRP a5317 HIS 0.009 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00459 (42522) covalent geometry : angle 0.75006 (58759) hydrogen bonds : bond 0.04174 ( 1738) hydrogen bonds : angle 4.60188 ( 5082) Misc. bond : bond 0.01627 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 676 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.9083 (t80) cc_final: 0.8810 (t80) REVERT: A 167 SER cc_start: 0.9185 (t) cc_final: 0.8696 (p) REVERT: A 187 GLN cc_start: 0.9308 (tp-100) cc_final: 0.9070 (tp-100) REVERT: B 15 ASP cc_start: 0.7937 (m-30) cc_final: 0.7572 (p0) REVERT: B 485 GLU cc_start: 0.4800 (OUTLIER) cc_final: 0.3208 (tp30) REVERT: C 95 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8858 (tp) REVERT: C 157 MET cc_start: 0.8360 (ttm) cc_final: 0.7890 (ttt) REVERT: C 313 GLN cc_start: 0.8542 (tt0) cc_final: 0.7976 (tp40) REVERT: C 356 MET cc_start: 0.9150 (tmm) cc_final: 0.8815 (tmm) REVERT: D 19 ASP cc_start: 0.8606 (t70) cc_final: 0.8295 (t0) REVERT: D 85 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8275 (tmm) REVERT: D 114 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8972 (mt) REVERT: D 126 MET cc_start: 0.8270 (tpp) cc_final: 0.8003 (tpp) REVERT: D 160 TYR cc_start: 0.9302 (t80) cc_final: 0.9072 (t80) REVERT: D 193 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8848 (tt) REVERT: D 241 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: D 279 LEU cc_start: 0.9044 (tp) cc_final: 0.8825 (tp) REVERT: D 295 SER cc_start: 0.8945 (t) cc_final: 0.8645 (p) REVERT: D 302 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7943 (pp20) REVERT: E 56 TYR cc_start: 0.7597 (m-80) cc_final: 0.7144 (m-80) REVERT: E 82 GLN cc_start: 0.7637 (mt0) cc_final: 0.7310 (pt0) REVERT: H 47 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7480 (mt-10) REVERT: I 1 MET cc_start: 0.7057 (mmm) cc_final: 0.6813 (mmp) REVERT: L 8 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8701 (mm-40) REVERT: a 5064 ARG cc_start: 0.6520 (mmm160) cc_final: 0.5874 (mtm180) REVERT: a 5098 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7059 (tm-30) REVERT: a 5103 ASP cc_start: 0.8278 (t70) cc_final: 0.7944 (t70) REVERT: a 5112 TYR cc_start: 0.8911 (t80) cc_final: 0.8419 (t80) REVERT: a 5183 MET cc_start: 0.8903 (mmt) cc_final: 0.8448 (mmm) REVERT: a 5187 GLN cc_start: 0.9414 (tp40) cc_final: 0.9104 (tp-100) REVERT: a 5261 GLN cc_start: 0.6469 (tt0) cc_final: 0.6112 (pp30) REVERT: a 5319 ASP cc_start: 0.8590 (m-30) cc_final: 0.8254 (t0) REVERT: b 5015 ASP cc_start: 0.7792 (m-30) cc_final: 0.7468 (p0) REVERT: b 5025 MET cc_start: 0.8793 (tpt) cc_final: 0.8536 (tpt) REVERT: b 5292 LEU cc_start: 0.7973 (pp) cc_final: 0.7673 (mt) REVERT: c 5095 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8537 (tp) REVERT: c 5187 ASP cc_start: 0.7375 (t0) cc_final: 0.6918 (t0) REVERT: c 5272 LEU cc_start: 0.9540 (tp) cc_final: 0.9324 (tp) REVERT: c 5282 MET cc_start: 0.8659 (mtm) cc_final: 0.7972 (mtm) REVERT: c 5348 GLU cc_start: 0.7391 (pt0) cc_final: 0.7188 (pt0) REVERT: d 5085 MET cc_start: 0.8812 (tmm) cc_final: 0.8266 (tmm) REVERT: d 5126 MET cc_start: 0.8306 (tpp) cc_final: 0.8016 (tpp) REVERT: d 5129 GLN cc_start: 0.9123 (tt0) cc_final: 0.8649 (mt0) REVERT: d 5160 TYR cc_start: 0.9344 (t80) cc_final: 0.8998 (t80) REVERT: d 5210 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8638 (tt) REVERT: d 5244 TYR cc_start: 0.8884 (p90) cc_final: 0.8583 (p90) REVERT: d 5295 SER cc_start: 0.9092 (t) cc_final: 0.8837 (p) REVERT: d 5333 ASP cc_start: 0.7762 (t70) cc_final: 0.7518 (t0) REVERT: e 5082 GLN cc_start: 0.7839 (mm110) cc_final: 0.7347 (pt0) REVERT: f 5041 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7365 (tm-30) REVERT: i 5001 MET cc_start: 0.6611 (mmt) cc_final: 0.6156 (mmp) REVERT: i 5002 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6515 (tm-30) REVERT: k 5038 VAL cc_start: 0.9398 (t) cc_final: 0.9175 (p) REVERT: m 5019 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8849 (p) REVERT: t 5006 TYR cc_start: 0.8434 (m-80) cc_final: 0.8100 (m-80) REVERT: t 5008 PHE cc_start: 0.9010 (t80) cc_final: 0.8602 (t80) REVERT: t 5012 CYS cc_start: 0.9005 (m) cc_final: 0.8687 (m) REVERT: t 5026 PRO cc_start: 0.8859 (Cg_exo) cc_final: 0.8644 (Cg_endo) REVERT: z 5001 MET cc_start: 0.6869 (tpp) cc_final: 0.6273 (ttp) REVERT: z 5039 LEU cc_start: 0.8833 (tp) cc_final: 0.8466 (mt) REVERT: Y 43 ARG cc_start: 0.8609 (mtp-110) cc_final: 0.8077 (mmp-170) REVERT: n 38 LEU cc_start: 0.9059 (mp) cc_final: 0.8737 (tp) REVERT: n 91 GLN cc_start: 0.8337 (tp-100) cc_final: 0.7841 (tm-30) REVERT: n 118 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7615 (tm-30) REVERT: N 91 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8526 (tm-30) REVERT: N 95 ASN cc_start: 0.8663 (p0) cc_final: 0.7989 (p0) REVERT: N 118 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6818 (tm-30) REVERT: N 119 GLN cc_start: 0.7485 (pp30) cc_final: 0.7257 (pp30) REVERT: N 122 LYS cc_start: 0.7574 (ptpp) cc_final: 0.7338 (ptpp) REVERT: y 25 ILE cc_start: 0.6217 (OUTLIER) cc_final: 0.5816 (mt) REVERT: y 43 ARG cc_start: 0.8839 (mtp85) cc_final: 0.7989 (mmp-170) outliers start: 161 outliers final: 116 residues processed: 773 average time/residue: 0.2253 time to fit residues: 301.2761 Evaluate side-chains 771 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 644 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 19 ASP Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5053 ILE Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5120 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5174 LEU Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5365 SER Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5060 ILE Chi-restraints excluded: chain c residue 5086 LEU Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5436 PHE Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain c residue 5472 LEU Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5213 ILE Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5281 MET Chi-restraints excluded: chain d residue 5282 SER Chi-restraints excluded: chain e residue 5025 ILE Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain l residue 5029 LEU Chi-restraints excluded: chain m residue 5009 ILE Chi-restraints excluded: chain m residue 5011 THR Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5001 MET Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain z residue 5004 LEU Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5050 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 16 SER Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 375 optimal weight: 2.9990 chunk 401 optimal weight: 5.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 285 optimal weight: 0.0980 chunk 394 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 404 optimal weight: 5.9990 chunk 410 optimal weight: 10.0000 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN E 74 GLN a5181 ASN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c5091 HIS ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c5382 ASN d5129 GLN l5004 ASN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z5058 ASN ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.122916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096981 restraints weight = 90726.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100475 restraints weight = 40195.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102732 restraints weight = 25375.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103955 restraints weight = 19453.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104853 restraints weight = 16816.881| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 42594 Z= 0.130 Angle : 0.731 13.427 58759 Z= 0.326 Chirality : 0.044 0.393 5783 Planarity : 0.005 0.054 7323 Dihedral : 16.549 174.654 8200 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 4.23 % Allowed : 21.66 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.13), residues: 4240 helix: 1.13 (0.10), residues: 2459 sheet: -0.29 (1.15), residues: 24 loop : -1.29 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG l5007 TYR 0.024 0.002 TYR t5006 PHE 0.044 0.001 PHE z5005 TRP 0.019 0.001 TRP a5317 HIS 0.009 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00292 (42522) covalent geometry : angle 0.73148 (58759) hydrogen bonds : bond 0.04000 ( 1738) hydrogen bonds : angle 4.52007 ( 5082) Misc. bond : bond 0.01903 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 709 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.8978 (t80) cc_final: 0.8694 (t80) REVERT: A 167 SER cc_start: 0.9200 (t) cc_final: 0.8584 (p) REVERT: A 319 ASP cc_start: 0.8298 (m-30) cc_final: 0.7912 (t0) REVERT: B 15 ASP cc_start: 0.7662 (m-30) cc_final: 0.7423 (p0) REVERT: B 330 MET cc_start: 0.8735 (mtp) cc_final: 0.8531 (tpp) REVERT: B 485 GLU cc_start: 0.5139 (OUTLIER) cc_final: 0.3366 (tp30) REVERT: C 119 LEU cc_start: 0.8786 (mt) cc_final: 0.8486 (mt) REVERT: C 157 MET cc_start: 0.8290 (ttm) cc_final: 0.8061 (ttt) REVERT: C 187 ASP cc_start: 0.8230 (t0) cc_final: 0.8027 (t0) REVERT: C 313 GLN cc_start: 0.8544 (tt0) cc_final: 0.7775 (tp40) REVERT: C 356 MET cc_start: 0.9150 (tmm) cc_final: 0.8799 (tmm) REVERT: D 19 ASP cc_start: 0.8557 (t70) cc_final: 0.8219 (t0) REVERT: D 43 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9105 (mm) REVERT: D 85 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8140 (tmm) REVERT: D 126 MET cc_start: 0.8317 (tpp) cc_final: 0.8110 (tpp) REVERT: D 160 TYR cc_start: 0.9247 (t80) cc_final: 0.8995 (t80) REVERT: D 193 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8803 (tt) REVERT: D 279 LEU cc_start: 0.8955 (tp) cc_final: 0.8720 (tp) REVERT: D 295 SER cc_start: 0.8983 (t) cc_final: 0.8644 (p) REVERT: D 302 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7880 (pp20) REVERT: E 32 ILE cc_start: 0.9280 (mm) cc_final: 0.8971 (tp) REVERT: E 56 TYR cc_start: 0.7447 (m-80) cc_final: 0.7106 (m-80) REVERT: H 47 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7387 (mt-10) REVERT: I 1 MET cc_start: 0.7018 (mmm) cc_final: 0.6594 (mmp) REVERT: L 8 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8591 (mm-40) REVERT: Z 19 MET cc_start: 0.8643 (tmm) cc_final: 0.8339 (tmm) REVERT: a 5064 ARG cc_start: 0.6296 (mmm160) cc_final: 0.5692 (mtm180) REVERT: a 5098 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6822 (tm-30) REVERT: a 5103 ASP cc_start: 0.8192 (t70) cc_final: 0.7838 (t70) REVERT: a 5112 TYR cc_start: 0.8826 (t80) cc_final: 0.8235 (t80) REVERT: a 5127 MET cc_start: 0.8641 (ttm) cc_final: 0.8425 (tpp) REVERT: a 5144 CYS cc_start: 0.7855 (t) cc_final: 0.7052 (t) REVERT: a 5172 MET cc_start: 0.9089 (ttm) cc_final: 0.8665 (ttt) REVERT: a 5187 GLN cc_start: 0.9447 (tp40) cc_final: 0.9232 (tp-100) REVERT: a 5261 GLN cc_start: 0.6563 (tt0) cc_final: 0.6363 (pp30) REVERT: a 5308 ASP cc_start: 0.7119 (p0) cc_final: 0.6534 (p0) REVERT: b 5015 ASP cc_start: 0.7535 (m-30) cc_final: 0.7293 (p0) REVERT: b 5025 MET cc_start: 0.8719 (tpt) cc_final: 0.8445 (tpt) REVERT: b 5256 MET cc_start: 0.8734 (tpp) cc_final: 0.8317 (tpp) REVERT: b 5292 LEU cc_start: 0.8005 (pp) cc_final: 0.7761 (mt) REVERT: b 5330 MET cc_start: 0.8603 (mtp) cc_final: 0.8329 (tpp) REVERT: c 5095 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8303 (tp) REVERT: c 5187 ASP cc_start: 0.7194 (t0) cc_final: 0.6743 (t0) REVERT: c 5282 MET cc_start: 0.8755 (mtm) cc_final: 0.7866 (mtm) REVERT: d 5042 TYR cc_start: 0.8515 (t80) cc_final: 0.8160 (t80) REVERT: d 5085 MET cc_start: 0.8684 (tmm) cc_final: 0.8158 (tmm) REVERT: d 5126 MET cc_start: 0.8361 (tpp) cc_final: 0.8051 (tpp) REVERT: d 5160 TYR cc_start: 0.9267 (t80) cc_final: 0.8925 (t80) REVERT: d 5210 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8458 (tt) REVERT: d 5222 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8585 (mp) REVERT: d 5244 TYR cc_start: 0.8648 (p90) cc_final: 0.8120 (p90) REVERT: d 5295 SER cc_start: 0.9066 (t) cc_final: 0.8782 (p) REVERT: d 5333 ASP cc_start: 0.7722 (t70) cc_final: 0.7465 (t0) REVERT: e 5075 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8199 (tm-30) REVERT: e 5082 GLN cc_start: 0.7747 (mm110) cc_final: 0.7245 (pt0) REVERT: f 5041 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7412 (tm-30) REVERT: k 5038 VAL cc_start: 0.9349 (t) cc_final: 0.9138 (p) REVERT: m 5019 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8849 (p) REVERT: t 5002 GLU cc_start: 0.8321 (tt0) cc_final: 0.7930 (tt0) REVERT: t 5006 TYR cc_start: 0.8354 (m-80) cc_final: 0.8067 (m-80) REVERT: t 5008 PHE cc_start: 0.8957 (t80) cc_final: 0.8542 (t80) REVERT: t 5012 CYS cc_start: 0.8968 (m) cc_final: 0.8649 (m) REVERT: z 5001 MET cc_start: 0.6651 (tpp) cc_final: 0.6177 (ttp) REVERT: z 5039 LEU cc_start: 0.8898 (tp) cc_final: 0.8511 (mt) REVERT: z 5058 ASN cc_start: 0.6848 (OUTLIER) cc_final: 0.6480 (m110) REVERT: n 91 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8360 (tm-30) REVERT: n 118 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7383 (tm-30) REVERT: n 119 GLN cc_start: 0.6316 (pp30) cc_final: 0.6012 (pp30) REVERT: N 91 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8389 (tm-30) REVERT: N 95 ASN cc_start: 0.8554 (p0) cc_final: 0.7920 (p0) REVERT: N 118 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7028 (tm-30) REVERT: N 119 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7177 (pp30) REVERT: N 122 LYS cc_start: 0.7597 (ptpp) cc_final: 0.7356 (ptpp) REVERT: y 25 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5766 (mt) REVERT: y 43 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8016 (mmp-170) REVERT: x 11 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7838 (t80) outliers start: 145 outliers final: 95 residues processed: 790 average time/residue: 0.2235 time to fit residues: 306.2356 Evaluate side-chains 774 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 666 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5120 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5174 LEU Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5055 MET Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5060 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5302 TYR Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain c residue 5472 LEU Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5222 LEU Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5281 MET Chi-restraints excluded: chain e residue 5025 ILE Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5026 VAL Chi-restraints excluded: chain l residue 5029 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5058 ASN Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain N residue 119 GLN Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 75 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 393 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 267 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS D 61 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN E 74 GLN a5130 GLN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e5074 GLN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 95 ASN ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 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 = 0.3765 r_free = 0.3765 target = 0.120485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094444 restraints weight = 92156.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097805 restraints weight = 41186.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100022 restraints weight = 26133.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101123 restraints weight = 20106.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102089 restraints weight = 17564.258| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 42594 Z= 0.190 Angle : 0.759 13.783 58759 Z= 0.340 Chirality : 0.045 0.412 5783 Planarity : 0.005 0.053 7323 Dihedral : 16.493 165.069 8200 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 4.20 % Allowed : 21.92 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.25 (0.13), residues: 4240 helix: 1.15 (0.10), residues: 2446 sheet: -0.33 (1.14), residues: 24 loop : -1.25 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG l5007 TYR 0.021 0.002 TYR D 296 PHE 0.037 0.002 PHE Z 5 TRP 0.029 0.001 TRP b5302 HIS 0.008 0.001 HIS b5201 Details of bonding type rmsd covalent geometry : bond 0.00429 (42522) covalent geometry : angle 0.75854 (58759) hydrogen bonds : bond 0.04094 ( 1738) hydrogen bonds : angle 4.56478 ( 5082) Misc. bond : bond 0.01602 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 678 time to evaluate : 1.323 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: A 38 ILE cc_start: 0.8961 (mm) cc_final: 0.8718 (mm) REVERT: A 112 TYR cc_start: 0.9077 (t80) cc_final: 0.8798 (t80) REVERT: A 167 SER cc_start: 0.9208 (t) cc_final: 0.8621 (p) REVERT: A 319 ASP cc_start: 0.8387 (m-30) cc_final: 0.7979 (t0) REVERT: B 15 ASP cc_start: 0.7798 (m-30) cc_final: 0.7557 (p0) REVERT: B 292 LEU cc_start: 0.7583 (pp) cc_final: 0.7359 (mt) REVERT: B 315 ILE cc_start: 0.8558 (tp) cc_final: 0.8308 (mm) REVERT: B 330 MET cc_start: 0.8752 (mtp) cc_final: 0.8533 (tpp) REVERT: B 485 GLU cc_start: 0.5247 (OUTLIER) cc_final: 0.3470 (tp30) REVERT: C 157 MET cc_start: 0.8248 (ttm) cc_final: 0.8006 (ttt) REVERT: C 313 GLN cc_start: 0.8698 (tt0) cc_final: 0.7916 (tp40) REVERT: C 356 MET cc_start: 0.9136 (tmm) cc_final: 0.8822 (tmm) REVERT: D 19 ASP cc_start: 0.8559 (t70) cc_final: 0.8229 (t0) REVERT: D 42 TYR cc_start: 0.8921 (t80) cc_final: 0.8703 (t80) REVERT: D 85 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8168 (tmm) REVERT: D 126 MET cc_start: 0.8374 (tpp) cc_final: 0.8147 (tpp) REVERT: D 160 TYR cc_start: 0.9283 (t80) cc_final: 0.9038 (t80) REVERT: D 193 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8786 (tt) REVERT: D 279 LEU cc_start: 0.9015 (tp) cc_final: 0.8767 (tp) REVERT: D 295 SER cc_start: 0.9012 (t) cc_final: 0.8707 (p) REVERT: D 302 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7965 (pp20) REVERT: E 32 ILE cc_start: 0.9251 (mm) cc_final: 0.8943 (tp) REVERT: E 56 TYR cc_start: 0.7635 (m-80) cc_final: 0.7406 (m-80) REVERT: H 47 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7437 (mt-10) REVERT: I 1 MET cc_start: 0.6994 (mmm) cc_final: 0.6767 (mmp) REVERT: L 8 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8583 (mm-40) REVERT: Z 1 MET cc_start: 0.8444 (ppp) cc_final: 0.5994 (mmt) REVERT: Z 19 MET cc_start: 0.8675 (tmm) cc_final: 0.8383 (tmm) REVERT: a 5064 ARG cc_start: 0.6363 (mmm160) cc_final: 0.5761 (mtm180) REVERT: a 5098 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6826 (tm-30) REVERT: a 5103 ASP cc_start: 0.8279 (t70) cc_final: 0.7931 (t70) REVERT: a 5112 TYR cc_start: 0.8928 (t80) cc_final: 0.8446 (t80) REVERT: a 5144 CYS cc_start: 0.7897 (t) cc_final: 0.7381 (t) REVERT: a 5187 GLN cc_start: 0.9421 (tp40) cc_final: 0.9136 (tp-100) REVERT: a 5194 MET cc_start: 0.8856 (mmm) cc_final: 0.8517 (mmm) REVERT: b 5015 ASP cc_start: 0.7684 (m-30) cc_final: 0.7447 (p0) REVERT: b 5025 MET cc_start: 0.8756 (tpt) cc_final: 0.8475 (tpt) REVERT: b 5292 LEU cc_start: 0.8097 (pp) cc_final: 0.7723 (mt) REVERT: b 5330 MET cc_start: 0.8618 (mtp) cc_final: 0.8359 (tpp) REVERT: c 5095 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8521 (tp) REVERT: c 5187 ASP cc_start: 0.7239 (t0) cc_final: 0.6834 (t0) REVERT: c 5282 MET cc_start: 0.8761 (mtm) cc_final: 0.7896 (mtm) REVERT: c 5293 ASN cc_start: 0.8672 (t0) cc_final: 0.8459 (t0) REVERT: d 5042 TYR cc_start: 0.8558 (t80) cc_final: 0.8238 (t80) REVERT: d 5049 LEU cc_start: 0.9488 (mt) cc_final: 0.9234 (mt) REVERT: d 5085 MET cc_start: 0.8732 (tmm) cc_final: 0.8004 (tmm) REVERT: d 5126 MET cc_start: 0.8334 (tpp) cc_final: 0.8021 (tpp) REVERT: d 5160 TYR cc_start: 0.9315 (t80) cc_final: 0.8966 (t80) REVERT: d 5210 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8531 (tt) REVERT: d 5222 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8549 (mp) REVERT: d 5295 SER cc_start: 0.9066 (t) cc_final: 0.8806 (p) REVERT: d 5333 ASP cc_start: 0.7746 (t70) cc_final: 0.7495 (t0) REVERT: e 5075 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8188 (tm-30) REVERT: e 5082 GLN cc_start: 0.7729 (mm110) cc_final: 0.7230 (pt0) REVERT: f 5041 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7371 (tm-30) REVERT: k 5038 VAL cc_start: 0.9355 (t) cc_final: 0.9152 (p) REVERT: m 5019 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8903 (p) REVERT: t 5002 GLU cc_start: 0.8291 (tt0) cc_final: 0.7935 (tt0) REVERT: t 5006 TYR cc_start: 0.8374 (m-80) cc_final: 0.8083 (m-80) REVERT: t 5008 PHE cc_start: 0.8944 (t80) cc_final: 0.8539 (t80) REVERT: t 5012 CYS cc_start: 0.8974 (m) cc_final: 0.8690 (m) REVERT: z 5001 MET cc_start: 0.6516 (tpp) cc_final: 0.6095 (ttp) REVERT: z 5039 LEU cc_start: 0.8879 (tp) cc_final: 0.8525 (mt) REVERT: z 5054 VAL cc_start: 0.8601 (t) cc_final: 0.8379 (p) REVERT: n 38 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8289 (mm) REVERT: n 91 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8405 (tm-30) REVERT: n 118 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7383 (tm-30) REVERT: n 119 GLN cc_start: 0.6460 (pp30) cc_final: 0.5999 (pp30) REVERT: N 91 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8441 (tm-30) REVERT: N 95 ASN cc_start: 0.8569 (p0) cc_final: 0.7904 (p0) REVERT: N 116 ARG cc_start: 0.6639 (mpp80) cc_final: 0.6325 (mpp80) REVERT: N 118 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6660 (tm-30) REVERT: N 119 GLN cc_start: 0.7471 (pp30) cc_final: 0.7175 (pp30) REVERT: N 122 LYS cc_start: 0.7508 (ptpp) cc_final: 0.7252 (ptpp) REVERT: y 25 ILE cc_start: 0.6301 (OUTLIER) cc_final: 0.5937 (mt) REVERT: y 43 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8003 (mmp-170) outliers start: 144 outliers final: 115 residues processed: 758 average time/residue: 0.2025 time to fit residues: 266.4281 Evaluate side-chains 779 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 654 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5120 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5174 LEU Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5055 MET Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5060 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5302 TYR Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5436 PHE Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain c residue 5472 LEU Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5222 LEU Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5281 MET Chi-restraints excluded: chain e residue 5025 ILE Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5028 ILE Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5026 VAL Chi-restraints excluded: chain l residue 5029 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 95 ASN Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 357 optimal weight: 0.6980 chunk 271 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.0370 chunk 388 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 336 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS D 61 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN a5130 GLN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c5091 HIS ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096110 restraints weight = 91268.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099199 restraints weight = 57174.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100317 restraints weight = 29953.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099908 restraints weight = 24841.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100304 restraints weight = 23982.079| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 42594 Z= 0.203 Angle : 0.844 59.195 58759 Z= 0.399 Chirality : 0.046 0.736 5783 Planarity : 0.005 0.225 7323 Dihedral : 16.505 164.978 8200 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.60 % Rotamer: Outliers : 4.00 % Allowed : 22.36 % Favored : 73.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 4240 helix: 1.17 (0.10), residues: 2446 sheet: -0.33 (1.14), residues: 24 loop : -1.24 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.142 0.001 ARG l5007 TYR 0.023 0.002 TYR D 296 PHE 0.030 0.001 PHE e5070 TRP 0.051 0.002 TRP c5189 HIS 0.007 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00462 (42522) covalent geometry : angle 0.84423 (58759) hydrogen bonds : bond 0.04147 ( 1738) hydrogen bonds : angle 4.56762 ( 5082) Misc. bond : bond 0.01656 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 654 time to evaluate : 0.871 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: A 38 ILE cc_start: 0.8964 (mm) cc_final: 0.8716 (mm) REVERT: A 112 TYR cc_start: 0.9070 (t80) cc_final: 0.8817 (t80) REVERT: A 167 SER cc_start: 0.9180 (t) cc_final: 0.8639 (p) REVERT: B 15 ASP cc_start: 0.7886 (m-30) cc_final: 0.7532 (p0) REVERT: B 315 ILE cc_start: 0.8548 (tp) cc_final: 0.8298 (mm) REVERT: B 330 MET cc_start: 0.8770 (mtp) cc_final: 0.8547 (tpp) REVERT: B 485 GLU cc_start: 0.4778 (OUTLIER) cc_final: 0.3235 (tp30) REVERT: C 157 MET cc_start: 0.8278 (ttm) cc_final: 0.8042 (ttt) REVERT: C 313 GLN cc_start: 0.8677 (tt0) cc_final: 0.7923 (tp40) REVERT: C 356 MET cc_start: 0.9130 (tmm) cc_final: 0.8802 (tmm) REVERT: D 19 ASP cc_start: 0.8581 (t70) cc_final: 0.8244 (t0) REVERT: D 42 TYR cc_start: 0.8905 (t80) cc_final: 0.8664 (t80) REVERT: D 43 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9070 (mm) REVERT: D 85 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8164 (tmm) REVERT: D 126 MET cc_start: 0.8348 (tpp) cc_final: 0.8100 (tpp) REVERT: D 160 TYR cc_start: 0.9260 (t80) cc_final: 0.9043 (t80) REVERT: D 193 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8800 (tt) REVERT: D 279 LEU cc_start: 0.9043 (tp) cc_final: 0.8793 (tp) REVERT: D 295 SER cc_start: 0.9010 (t) cc_final: 0.8728 (p) REVERT: D 302 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8013 (pp20) REVERT: E 32 ILE cc_start: 0.9225 (mm) cc_final: 0.8923 (tp) REVERT: E 56 TYR cc_start: 0.7783 (m-80) cc_final: 0.7515 (m-80) REVERT: H 47 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7484 (mt-10) REVERT: I 1 MET cc_start: 0.7040 (mmm) cc_final: 0.6812 (mmp) REVERT: L 8 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8623 (mm-40) REVERT: Z 1 MET cc_start: 0.8441 (ppp) cc_final: 0.6000 (mmt) REVERT: Z 19 MET cc_start: 0.8640 (tmm) cc_final: 0.8346 (tmm) REVERT: a 5064 ARG cc_start: 0.6423 (mmm160) cc_final: 0.5816 (mtm180) REVERT: a 5098 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6959 (tm-30) REVERT: a 5103 ASP cc_start: 0.8303 (t70) cc_final: 0.7955 (t70) REVERT: a 5112 TYR cc_start: 0.8921 (t80) cc_final: 0.8440 (t80) REVERT: a 5187 GLN cc_start: 0.9430 (tp40) cc_final: 0.9143 (tp-100) REVERT: a 5194 MET cc_start: 0.8895 (mmm) cc_final: 0.8549 (mmm) REVERT: b 5015 ASP cc_start: 0.7758 (m-30) cc_final: 0.7479 (p0) REVERT: b 5025 MET cc_start: 0.8764 (tpt) cc_final: 0.8498 (tpt) REVERT: b 5292 LEU cc_start: 0.8239 (pp) cc_final: 0.7899 (mt) REVERT: b 5330 MET cc_start: 0.8655 (mtp) cc_final: 0.8370 (tpp) REVERT: c 5095 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8531 (tp) REVERT: c 5187 ASP cc_start: 0.7311 (t0) cc_final: 0.6859 (t0) REVERT: c 5282 MET cc_start: 0.8651 (mtm) cc_final: 0.7881 (mtm) REVERT: d 5042 TYR cc_start: 0.8535 (t80) cc_final: 0.8212 (t80) REVERT: d 5049 LEU cc_start: 0.9488 (mt) cc_final: 0.9238 (mt) REVERT: d 5085 MET cc_start: 0.8561 (tmm) cc_final: 0.7998 (tmm) REVERT: d 5126 MET cc_start: 0.8307 (tpp) cc_final: 0.7984 (tpp) REVERT: d 5160 TYR cc_start: 0.9303 (t80) cc_final: 0.8967 (t80) REVERT: d 5210 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8588 (tt) REVERT: d 5295 SER cc_start: 0.9070 (t) cc_final: 0.8839 (p) REVERT: d 5333 ASP cc_start: 0.7747 (t70) cc_final: 0.7488 (t0) REVERT: e 5075 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8164 (tm-30) REVERT: e 5082 GLN cc_start: 0.7962 (mm110) cc_final: 0.7309 (pt0) REVERT: f 5041 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7382 (tm-30) REVERT: k 5038 VAL cc_start: 0.9353 (t) cc_final: 0.9151 (p) REVERT: m 5019 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8915 (p) REVERT: t 5002 GLU cc_start: 0.8404 (tt0) cc_final: 0.7861 (tt0) REVERT: t 5006 TYR cc_start: 0.8328 (m-80) cc_final: 0.7867 (m-80) REVERT: t 5008 PHE cc_start: 0.8963 (t80) cc_final: 0.8544 (t80) REVERT: t 5012 CYS cc_start: 0.8991 (m) cc_final: 0.8686 (m) REVERT: z 5001 MET cc_start: 0.6484 (tpp) cc_final: 0.6093 (ttp) REVERT: z 5039 LEU cc_start: 0.8878 (tp) cc_final: 0.8532 (mt) REVERT: z 5054 VAL cc_start: 0.8745 (t) cc_final: 0.8538 (p) REVERT: n 38 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8201 (mm) REVERT: n 91 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8380 (tm-30) REVERT: n 95 ASN cc_start: 0.8796 (m110) cc_final: 0.8444 (m-40) REVERT: n 118 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7659 (tm-30) REVERT: n 119 GLN cc_start: 0.6455 (pp30) cc_final: 0.6058 (pp30) REVERT: N 91 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8480 (tm-30) REVERT: N 95 ASN cc_start: 0.8645 (p0) cc_final: 0.7952 (p0) REVERT: N 118 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6663 (tm-30) REVERT: N 119 GLN cc_start: 0.7535 (pp30) cc_final: 0.7205 (pp30) REVERT: N 122 LYS cc_start: 0.7460 (ptpp) cc_final: 0.7197 (ptpp) REVERT: y 25 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.5977 (mt) REVERT: y 43 ARG cc_start: 0.8854 (mtp85) cc_final: 0.7981 (mmp-170) outliers start: 137 outliers final: 118 residues processed: 732 average time/residue: 0.1826 time to fit residues: 233.0610 Evaluate side-chains 779 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 651 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 302 GLU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5037 MET Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5120 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5174 LEU Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5055 MET Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5060 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5265 ILE Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5302 TYR Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5436 PHE Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain c residue 5472 LEU Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5199 MET Chi-restraints excluded: chain d residue 5205 LEU Chi-restraints excluded: chain d residue 5210 LEU Chi-restraints excluded: chain d residue 5211 CYS Chi-restraints excluded: chain d residue 5231 THR Chi-restraints excluded: chain d residue 5272 LEU Chi-restraints excluded: chain d residue 5281 MET Chi-restraints excluded: chain e residue 5025 ILE Chi-restraints excluded: chain e residue 5063 ILE Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain f residue 5023 VAL Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain i residue 5031 ASN Chi-restraints excluded: chain k residue 5028 ILE Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain l residue 5029 LEU Chi-restraints excluded: chain m residue 5019 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5050 LEU Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain y residue 25 ILE Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain x residue 11 PHE Chi-restraints excluded: chain x residue 16 SER Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 25 PHE Chi-restraints excluded: chain x residue 36 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 393 optimal weight: 50.0000 chunk 217 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 332 optimal weight: 0.9990 chunk 340 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN a5130 GLN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c5091 HIS ** c5229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.121768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095671 restraints weight = 91495.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.099129 restraints weight = 40865.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101351 restraints weight = 25910.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102722 restraints weight = 19935.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103354 restraints weight = 17068.141| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 42594 Z= 0.154 Angle : 0.753 13.991 58759 Z= 0.339 Chirality : 0.045 0.407 5783 Planarity : 0.005 0.063 7323 Dihedral : 16.312 154.780 8200 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 4.06 % Allowed : 22.12 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.13), residues: 4240 helix: 1.12 (0.10), residues: 2471 sheet: -0.28 (1.15), residues: 24 loop : -1.27 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.000 ARG l5007 TYR 0.027 0.002 TYR D 296 PHE 0.035 0.001 PHE e5070 TRP 0.034 0.001 TRP b5302 HIS 0.007 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00348 (42522) covalent geometry : angle 0.75334 (58759) hydrogen bonds : bond 0.04063 ( 1738) hydrogen bonds : angle 4.50202 ( 5082) Misc. bond : bond 0.01692 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8269.44 seconds wall clock time: 143 minutes 51.91 seconds (8631.91 seconds total)