Starting phenix.real_space_refine on Sun Mar 24 18:52:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/03_2024/7czl_30511_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/03_2024/7czl_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/03_2024/7czl_30511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/03_2024/7czl_30511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/03_2024/7czl_30511_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czl_30511/03_2024/7czl_30511_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 16": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "K ARG 46": "NH1" <-> "NH2" Residue "T ARG 28": "NH1" <-> "NH2" Residue "a ARG 5016": "NH1" <-> "NH2" Residue "a PHE 5300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 5057": "NH1" <-> "NH2" Residue "b ARG 5068": "NH1" <-> "NH2" Residue "b ARG 5384": "NH1" <-> "NH2" Residue "b ARG 5385": "NH1" <-> "NH2" Residue "b ARG 5472": "NH1" <-> "NH2" Residue "c ARG 5207": "NH1" <-> "NH2" Residue "c ARG 5261": "NH1" <-> "NH2" Residue "c ARG 5320": "NH1" <-> "NH2" Residue "c ARG 5362": "NH1" <-> "NH2" Residue "c ARG 5390": "NH1" <-> "NH2" Residue "c ARG 5461": "NH1" <-> "NH2" Residue "e ARG 5051": "NH1" <-> "NH2" Residue "i ARG 5034": "NH1" <-> "NH2" Residue "t ARG 5028": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 76": "NH1" <-> "NH2" Residue "n ARG 82": "NH1" <-> "NH2" Residue "n ARG 107": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "y ARG 42": "NH1" <-> "NH2" Residue "y ARG 43": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: {'GLN:plan1': 1, 'ARG:plan': 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, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2} 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-4': 1, 'PQ9:plan-2': 1, 'PQ9:plan-3': 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: 20.26, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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=71, symmetry=0 Number of additional bonds: simple=71, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.79 Conformation dependent library (CDL) restraints added in 6.4 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... running ksdssp... Secondary structure from input PDB file: 173 helices and 6 sheets defined 57.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 32 through 53 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 102 through 107 Processing helix chain 'A' and resid 110 through 134 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 143 through 157 removed outlier: 4.131A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.757A pdb=" N PHE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 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 248 through 258 removed outlier: 3.649A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 268 through 294 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) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.721A pdb=" N VAL A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.507A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 43 removed outlier: 3.503A pdb=" N ALA B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 93 through 116 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 135 through 155 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 187 through 190 removed outlier: 3.680A pdb=" N PHE B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 195 through 218 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 223 through 229 Processing helix chain 'B' and resid 234 through 257 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 272 through 276 removed outlier: 3.630A pdb=" N ASP B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 276' Processing helix chain 'B' and resid 279 through 294 removed outlier: 4.274A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.575A pdb=" N ASP B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.696A pdb=" N ILE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 476 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 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.696A pdb=" N GLY C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 108 through 133 removed outlier: 3.514A pdb=" N VAL C 114 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 116 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY C 126 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 132 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 156 through 180 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 210 through 213 No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 230 through 252 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 258 through 262 Processing helix chain 'C' and resid 268 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 299 through 302 No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 306 through 323 removed outlier: 3.649A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'C' and resid 364 through 369 Proline residue: C 368 - end of helix No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.664A pdb=" N ASN C 382 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 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) Processing helix chain 'C' and resid 422 through 453 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 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 32 through 53 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 106 Processing helix chain 'D' and resid 109 through 136 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 141 through 157 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 159 through 163 Processing helix chain 'D' and resid 175 through 188 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 195 through 220 removed outlier: 3.632A pdb=" N GLY D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.501A pdb=" N ILE D 256 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 290 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) Processing helix chain 'D' and resid 299 through 307 Processing helix chain 'D' and resid 316 through 333 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 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 26 through 39 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 42 through 47 Processing helix chain 'E' and resid 72 through 82 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) Processing helix chain 'F' and resid 20 through 41 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) Processing helix chain 'H' and resid 6 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 29 through 49 Processing helix chain 'I' and resid 2 through 24 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 19 through 23 Processing helix chain 'K' and resid 28 through 43 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 14 through 36 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 7 through 31 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 22 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 28 removed outlier: 3.684A pdb=" N VAL Z 13 " --> pdb=" O LEU Z 9 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 33 through 36 No H-bonds generated for 'chain 'Z' and resid 33 through 36' Processing helix chain 'Z' and resid 39 through 61 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 5022 Processing helix chain 'a' and resid 5032 through 5053 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 5102 through 5107 Processing helix chain 'a' and resid 5110 through 5134 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 5143 through 5157 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 5160 through 5165 Processing helix chain 'a' and resid 5168 through 5170 No H-bonds generated for 'chain 'a' and resid 5168 through 5170' Processing helix chain 'a' and resid 5176 through 5190 removed outlier: 3.757A pdb=" N PHE a5180 " --> pdb=" O ILE a5176 " (cutoff:3.500A) Processing helix chain 'a' and resid 5196 through 5221 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 5248 through 5258 removed outlier: 3.649A pdb=" N GLY a5253 " --> pdb=" O VAL a5249 " (cutoff:3.500A) Processing helix chain 'a' and resid 5261 through 5263 No H-bonds generated for 'chain 'a' and resid 5261 through 5263' Processing helix chain 'a' and resid 5268 through 5294 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) Processing helix chain 'a' and resid 5317 through 5332 removed outlier: 3.721A pdb=" N VAL a5330 " --> pdb=" O LEU a5326 " (cutoff:3.500A) Processing helix chain 'b' and resid 5008 through 5012 removed outlier: 3.506A pdb=" N VAL b5011 " --> pdb=" O VAL b5008 " (cutoff:3.500A) Processing helix chain 'b' and resid 5016 through 5043 removed outlier: 3.503A pdb=" N ALA b5038 " --> pdb=" O ALA b5034 " (cutoff:3.500A) Processing helix chain 'b' and resid 5063 through 5069 Processing helix chain 'b' and resid 5093 through 5116 Processing helix chain 'b' and resid 5121 through 5123 No H-bonds generated for 'chain 'b' and resid 5121 through 5123' Processing helix chain 'b' and resid 5135 through 5155 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 5187 through 5190 removed outlier: 3.679A pdb=" N PHE b5190 " --> pdb=" O PRO b5187 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5187 through 5190' Processing helix chain 'b' and resid 5195 through 5218 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 5223 through 5229 Processing helix chain 'b' and resid 5234 through 5257 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 5272 through 5276 removed outlier: 3.629A pdb=" N ASP b5276 " --> pdb=" O ARG b5272 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5272 through 5276' Processing helix chain 'b' and resid 5279 through 5294 removed outlier: 4.273A pdb=" N ARG b5287 " --> pdb=" O GLU b5283 " (cutoff:3.500A) Processing helix chain 'b' and resid 5298 through 5303 Processing helix chain 'b' and resid 5307 through 5312 Processing helix chain 'b' and resid 5330 through 5334 removed outlier: 3.576A pdb=" N ASP b5334 " --> pdb=" O ASN b5331 " (cutoff:3.500A) Processing helix chain 'b' and resid 5392 through 5395 No H-bonds generated for 'chain 'b' and resid 5392 through 5395' Processing helix chain 'b' and resid 5414 through 5426 removed outlier: 3.696A pdb=" N ILE b5425 " --> pdb=" O ALA b5421 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE b5426 " --> pdb=" O ARG b5422 " (cutoff:3.500A) Processing helix chain 'b' and resid 5447 through 5476 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 5478 through 5480 No H-bonds generated for 'chain 'b' and resid 5478 through 5480' Processing helix chain 'c' and resid 5038 through 5042 Processing helix chain 'c' and resid 5046 through 5073 removed outlier: 3.697A pdb=" N GLY c5051 " --> pdb=" O GLY c5047 " (cutoff:3.500A) Processing helix chain 'c' and resid 5082 through 5084 No H-bonds generated for 'chain 'c' and resid 5082 through 5084' Processing helix chain 'c' and resid 5089 through 5095 Processing helix chain 'c' and resid 5101 through 5103 No H-bonds generated for 'chain 'c' and resid 5101 through 5103' Processing helix chain 'c' and resid 5108 through 5133 removed outlier: 3.514A pdb=" N VAL c5114 " --> pdb=" O PHE c5111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL c5116 " --> pdb=" O VAL c5113 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY c5126 " --> pdb=" O ALA c5123 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS c5132 " --> pdb=" O GLY c5129 " (cutoff:3.500A) Processing helix chain 'c' and resid 5140 through 5143 No H-bonds generated for 'chain 'c' and resid 5140 through 5143' Processing helix chain 'c' and resid 5156 through 5180 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 5210 through 5213 No H-bonds generated for 'chain 'c' and resid 5210 through 5213' Processing helix chain 'c' and resid 5230 through 5252 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 5258 through 5262 Processing helix chain 'c' and resid 5268 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 5299 through 5302 No H-bonds generated for 'chain 'c' and resid 5299 through 5302' Processing helix chain 'c' and resid 5306 through 5323 removed outlier: 3.650A pdb=" N SER c5310 " --> pdb=" O GLY c5306 " (cutoff:3.500A) Processing helix chain 'c' and resid 5353 through 5357 Processing helix chain 'c' and resid 5364 through 5369 Proline residue: c5368 - end of helix No H-bonds generated for 'chain 'c' and resid 5364 through 5369' Processing helix chain 'c' and resid 5377 through 5383 removed outlier: 3.663A pdb=" N ASN c5382 " --> pdb=" O ASN c5378 " (cutoff:3.500A) Processing helix chain 'c' and resid 5386 through 5397 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) Processing helix chain 'c' and resid 5422 through 5453 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 5457 No H-bonds generated for 'chain 'c' and resid 5455 through 5457' Processing helix chain 'd' and resid 5014 through 5022 Processing helix chain 'd' and resid 5032 through 5053 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 5106 Processing helix chain 'd' and resid 5109 through 5136 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 5141 through 5157 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 5159 through 5163 Processing helix chain 'd' and resid 5175 through 5188 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 5195 through 5220 removed outlier: 3.632A pdb=" N GLY d5200 " --> pdb=" O PHE d5196 " (cutoff:3.500A) Processing helix chain 'd' and resid 5246 through 5256 removed outlier: 3.501A pdb=" N ILE d5256 " --> pdb=" O PHE d5252 " (cutoff:3.500A) Processing helix chain 'd' and resid 5264 through 5290 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) Processing helix chain 'd' and resid 5299 through 5307 Processing helix chain 'd' and resid 5316 through 5333 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 5022 through 5024 No H-bonds generated for 'chain 'e' and resid 5022 through 5024' Processing helix chain 'e' and resid 5026 through 5039 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 5042 through 5047 Processing helix chain 'e' and resid 5072 through 5082 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) Processing helix chain 'f' and resid 5018 through 5041 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) Processing helix chain 'h' and resid 5006 through 5012 removed outlier: 3.543A pdb=" N ARG h5012 " --> pdb=" O GLY h5008 " (cutoff:3.500A) Processing helix chain 'h' and resid 5029 through 5049 Processing helix chain 'i' and resid 5002 through 5024 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 5019 through 5023 Processing helix chain 'k' and resid 5028 through 5043 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 5014 through 5036 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 5007 through 5031 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 5022 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 5028 removed outlier: 3.683A pdb=" N VAL z5013 " --> pdb=" O LEU z5009 " (cutoff:3.500A) Proline residue: z5024 - end of helix Processing helix chain 'z' and resid 5033 through 5036 No H-bonds generated for 'chain 'z' and resid 5033 through 5036' Processing helix chain 'z' and resid 5039 through 5061 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 21 through 41 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 33 through 47 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 58 through 76 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) Processing helix chain 'n' and resid 85 through 104 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 111 through 132 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 33 through 47 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 58 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 85 through 104 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 111 through 132 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 20 through 28 Processing helix chain 'y' and resid 31 through 42 Processing helix chain 'X' and resid 5 through 34 Processing helix chain 'x' and resid 5 through 34 removed outlier: 3.643A pdb=" N PHE x 25 " --> pdb=" O LEU x 21 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.683A pdb=" N VAL B 345 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 369 through 371 Processing sheet with id= C, first strand: chain 'C' and resid 341 through 343 Processing sheet with id= D, first strand: chain 'b' and resid 5343 through 5347 removed outlier: 3.684A pdb=" N VAL b5345 " --> pdb=" O SER b5400 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b' and resid 5369 through 5371 Processing sheet with id= F, first strand: chain 'c' and resid 5341 through 5343 1506 hydrogen bonds defined for protein. 4356 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: 11.94 Time building geometry restraints manager: 19.13 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: 85.28 - 103.77: 1090 103.77 - 122.25: 49323 122.25 - 140.73: 8128 140.73 - 159.21: 74 159.21 - 177.69: 144 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: 21876 34.90 - 69.81: 931 69.81 - 104.71: 168 104.71 - 139.62: 177 139.62 - 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: 7335 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C12 BCR c5514 " -0.248 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C13 BCR c5514 " 0.197 2.00e-02 2.50e+03 pdb=" C14 BCR c5514 " 0.486 2.00e-02 2.50e+03 pdb=" C15 BCR c5514 " -0.360 2.00e-02 2.50e+03 pdb=" C35 BCR c5514 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 BCR Y 101 " 0.153 2.00e-02 2.50e+03 2.80e-01 7.85e+02 pdb=" C15 BCR Y 101 " -0.409 2.00e-02 2.50e+03 pdb=" C16 BCR Y 101 " 0.341 2.00e-02 2.50e+03 pdb=" C17 BCR Y 101 " -0.086 2.00e-02 2.50e+03 ... (remaining 7332 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 18 1.99 - 2.72: 3153 2.72 - 3.44: 62375 3.44 - 4.17: 99603 4.17 - 4.90: 177374 Nonbonded interactions: 342523 Sorted by model distance: nonbonded pdb=" OE2 GLU m5002 " pdb=" O4' LMT m5102 " model vdw 1.261 2.440 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 342518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 5485 or resid 5601 through 5618)) } ncs_group { reference = (chain 'C' and (resid 27 through 472 or resid 501 through 510 or (resid 511 and \ (name NB or name ND or name C1 or name C1A or name C1B or name C1C or name C1D o \ r 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 C6 or name CAA or name CAB or name CAC or nam \ e 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 CM \ B 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 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 C2 \ A 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 n \ ame C5 or name CAA or name CAB or name CAC or name CAD or name CBA or name CBB o \ r name CBC or name CBD or name CED or name CGA or name CGD or name CHA or name C \ HB or name CHC or name CHD or name CMA or name CMB or name CMC or name CMD or na \ me 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 5472 or resid 5501 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 351 or resid 401 through 402 or (r \ esid 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 C \ 3 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 n \ ame 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 nam \ e O2A or name O2D or name OBD or name MG )) or resid 408 through 410)) selection = (chain 'd' and (resid 5013 through 5351 or resid 5401 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 44 or resid 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.030 Extract box with map and model: 5.470 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 100.210 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.520 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.640 ------------------------------------------------------------------------------- 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 : 0.012 0.135 42522 Z= 0.691 Angle : 1.232 17.176 58759 Z= 0.531 Chirality : 0.063 0.736 5783 Planarity : 0.023 0.307 7335 Dihedral : 21.656 174.524 15372 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 28.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.055 0.003 TRP A 142 HIS 0.018 0.003 HIS b5343 PHE 0.040 0.003 PHE B 462 TYR 0.096 0.004 TYR b5258 ARG 0.011 0.001 ARG B 472 *********************** 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 fitting. rotamer outliers: 56 poor density : 991 time to evaluate : 4.033 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: A 42 LEU cc_start: 0.8901 (tt) cc_final: 0.8464 (tp) REVERT: A 226 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6377 (tm-30) REVERT: A 246 TYR cc_start: 0.7098 (p90) cc_final: 0.6856 (p90) REVERT: A 269 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8605 (mtm180) REVERT: B 485 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.3741 (tp30) REVERT: C 218 PHE cc_start: 0.7561 (m-80) cc_final: 0.7206 (m-10) REVERT: C 265 ILE cc_start: 0.9252 (mm) cc_final: 0.9052 (tp) REVERT: C 272 LEU cc_start: 0.9644 (tp) cc_final: 0.9416 (tp) REVERT: D 211 CYS cc_start: 0.8999 (t) cc_final: 0.8791 (t) REVERT: D 244 TYR cc_start: 0.8904 (p90) cc_final: 0.8587 (p90) REVERT: E 67 THR cc_start: 0.8023 (m) cc_final: 0.7621 (p) REVERT: I 1 MET cc_start: 0.6292 (mmm) cc_final: 0.5948 (mmp) REVERT: I 5 LYS cc_start: 0.8986 (tttt) cc_final: 0.8551 (tttm) REVERT: I 10 ILE cc_start: 0.9272 (mm) cc_final: 0.8856 (mt) REVERT: K 28 ILE cc_start: 0.8827 (pt) cc_final: 0.8603 (mp) REVERT: L 4 ASN cc_start: 0.8043 (t0) cc_final: 0.7782 (t0) REVERT: L 16 SER cc_start: 0.9029 (m) cc_final: 0.8779 (t) REVERT: M 16 LEU cc_start: 0.9110 (mp) cc_final: 0.8779 (mp) REVERT: Z 59 PHE cc_start: 0.8182 (t80) cc_final: 0.7955 (t80) REVERT: a 5112 TYR cc_start: 0.8966 (t80) cc_final: 0.8745 (t80) REVERT: a 5180 PHE cc_start: 0.9190 (m-10) cc_final: 0.8910 (m-10) REVERT: a 5193 LEU cc_start: 0.9297 (mt) cc_final: 0.9029 (mt) REVERT: a 5194 MET cc_start: 0.8426 (mmm) cc_final: 0.7998 (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: 0.7863 (t0) REVERT: b 5025 MET cc_start: 0.8651 (tpt) cc_final: 0.8079 (tpt) REVERT: c 5091 HIS cc_start: 0.8367 (m90) cc_final: 0.8164 (m-70) REVERT: c 5230 LEU cc_start: 0.8441 (mt) cc_final: 0.8046 (mp) REVERT: c 5282 MET cc_start: 0.9007 (mtp) cc_final: 0.8536 (mtp) REVERT: c 5288 CYS cc_start: 0.8014 (t) cc_final: 0.7782 (t) REVERT: c 5297 TYR cc_start: 0.7806 (m-80) cc_final: 0.7478 (m-80) REVERT: e 5067 THR cc_start: 0.7566 (m) cc_final: 0.7222 (p) REVERT: m 5015 VAL cc_start: 0.9525 (t) cc_final: 0.9276 (t) REVERT: m 5016 LEU cc_start: 0.8786 (mp) cc_final: 0.8478 (mp) REVERT: Y 43 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7731 (tpp-160) REVERT: y 23 THR cc_start: 0.4391 (OUTLIER) cc_final: 0.4190 (p) REVERT: x 11 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7925 (t80) outliers start: 56 outliers final: 34 residues processed: 1024 average time/residue: 0.5372 time to fit residues: 905.3390 Evaluate side-chains 654 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 616 time to evaluate : 3.973 ------------------------------------------------------------------------------- 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 350 optimal weight: 5.9990 chunk 314 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 125 optimal weight: 0.2980 chunk 197 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 376 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 322 ASN A 325 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 D 61 HIS ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN E 23 HIS H 59 ASN K 40 GLN L 8 GLN Z 58 ASN a5075 ASN a5087 ASN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5296 ASN a5322 ASN ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5274 GLN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b5289 GLN b5317 ASN b5343 HIS c5084 GLN c5311 GLN c5382 ASN d5061 HIS d5129 GLN d5334 GLN e5023 HIS h5059 ASN k5040 GLN l5008 GLN ** m5032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 GLN n 100 HIS n 119 GLN N 100 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 42522 Z= 0.240 Angle : 0.915 17.694 58759 Z= 0.398 Chirality : 0.048 0.361 5783 Planarity : 0.006 0.063 7335 Dihedral : 23.042 179.467 8267 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 4.14 % Allowed : 10.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4240 helix: -0.58 (0.10), residues: 2343 sheet: -1.87 (0.98), residues: 24 loop : -1.56 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP a5317 HIS 0.014 0.002 HIS A 272 PHE 0.034 0.002 PHE X 10 TYR 0.031 0.002 TYR m5026 ARG 0.012 0.001 ARG n 76 *********************** 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 978 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 836 time to evaluate : 3.609 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: A 226 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6211 (tm-30) REVERT: A 328 MET cc_start: 0.7875 (mmp) cc_final: 0.7498 (mtm) REVERT: B 256 MET cc_start: 0.8256 (tpp) cc_final: 0.8032 (tpp) REVERT: B 410 THR cc_start: 0.7460 (m) cc_final: 0.7145 (p) REVERT: B 485 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.4381 (tp30) REVERT: C 313 GLN cc_start: 0.8040 (tt0) cc_final: 0.7799 (pp30) REVERT: D 19 ASP cc_start: 0.8294 (t70) cc_final: 0.7991 (t0) REVERT: D 129 GLN cc_start: 0.9005 (tt0) cc_final: 0.8570 (tt0) REVERT: H 31 MET cc_start: 0.8229 (tmm) cc_final: 0.7970 (tmm) REVERT: I 1 MET cc_start: 0.6341 (mmm) cc_final: 0.5639 (mmt) REVERT: I 10 ILE cc_start: 0.9083 (mm) cc_final: 0.8693 (mt) REVERT: I 19 PHE cc_start: 0.8814 (t80) cc_final: 0.8112 (t80) REVERT: I 21 PHE cc_start: 0.8466 (m-10) cc_final: 0.8168 (m-80) REVERT: T 3 THR cc_start: 0.9265 (m) cc_final: 0.8910 (p) REVERT: T 6 TYR cc_start: 0.8418 (m-80) cc_final: 0.8036 (m-80) REVERT: T 8 PHE cc_start: 0.8706 (t80) cc_final: 0.8376 (t80) REVERT: a 5064 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5623 (mtm180) REVERT: a 5112 TYR cc_start: 0.8624 (t80) cc_final: 0.8210 (t80) REVERT: a 5172 MET cc_start: 0.8873 (ttm) cc_final: 0.8554 (ttt) REVERT: a 5187 GLN cc_start: 0.9073 (tp40) cc_final: 0.8752 (tp-100) REVERT: a 5261 GLN cc_start: 0.6589 (tt0) cc_final: 0.6384 (pp30) REVERT: a 5319 ASP cc_start: 0.8196 (m-30) cc_final: 0.7800 (t0) REVERT: b 5025 MET cc_start: 0.8774 (tpt) cc_final: 0.8570 (tpt) REVERT: b 5188 ASP cc_start: 0.8066 (p0) cc_final: 0.7724 (p0) REVERT: b 5256 MET cc_start: 0.8232 (tpp) cc_final: 0.7805 (tpp) REVERT: c 5340 TYR cc_start: 0.6989 (m-80) cc_final: 0.6288 (m-10) REVERT: d 5098 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: d 5126 MET cc_start: 0.8379 (tpp) cc_final: 0.8138 (tpp) REVERT: d 5129 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: d 5210 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8381 (tt) REVERT: d 5333 ASP cc_start: 0.7493 (t70) cc_final: 0.7065 (t0) REVERT: i 5001 MET cc_start: 0.6409 (mmt) cc_final: 0.5255 (mmp) REVERT: i 5019 PHE cc_start: 0.8871 (t80) cc_final: 0.8389 (t80) REVERT: i 5021 PHE cc_start: 0.8449 (m-10) cc_final: 0.8129 (m-80) REVERT: l 5004 ASN cc_start: 0.7208 (t0) cc_final: 0.6973 (t0) REVERT: m 5015 VAL cc_start: 0.9479 (t) cc_final: 0.8986 (t) REVERT: m 5019 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8651 (p) REVERT: t 5008 PHE cc_start: 0.8774 (t80) cc_final: 0.8558 (t80) REVERT: t 5019 PHE cc_start: 0.8554 (t80) cc_final: 0.8315 (t80) REVERT: t 5026 PRO cc_start: 0.7945 (Cg_endo) cc_final: 0.7333 (Cg_exo) REVERT: Y 42 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7280 (ptp-170) REVERT: Y 43 ARG cc_start: 0.8462 (mtp-110) cc_final: 0.8000 (mmp-170) REVERT: y 43 ARG cc_start: 0.8747 (mtp85) cc_final: 0.8177 (mmp-170) REVERT: x 15 LEU cc_start: 0.9320 (tm) cc_final: 0.9107 (tt) outliers start: 142 outliers final: 78 residues processed: 909 average time/residue: 0.4833 time to fit residues: 745.2065 Evaluate side-chains 741 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 656 time to evaluate : 4.027 ------------------------------------------------------------------------------- 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 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 371 THR 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 243 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 28 VAL 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 L residue 13 ASN Chi-restraints excluded: chain M residue 11 THR 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 5288 LEU Chi-restraints excluded: chain b residue 5024 LEU Chi-restraints excluded: chain b residue 5203 ILE Chi-restraints excluded: chain b residue 5214 LEU Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5371 THR 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 5249 ILE Chi-restraints excluded: chain c residue 5354 GLU 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 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5098 GLN 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 e residue 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5070 PHE 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 5019 SER Chi-restraints excluded: chain m residue 5031 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 50 LEU 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 36 LYS 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 209 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 377 optimal weight: 0.9990 chunk 407 optimal weight: 20.0000 chunk 336 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a5234 ASN ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c5441 HIS d5129 GLN ** d5189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d5301 GLN k5040 GLN m5032 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42522 Z= 0.277 Angle : 0.813 15.400 58759 Z= 0.357 Chirality : 0.046 0.339 5783 Planarity : 0.005 0.062 7335 Dihedral : 19.623 178.330 8220 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 5.43 % Allowed : 14.13 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4240 helix: 0.21 (0.10), residues: 2367 sheet: -1.54 (1.03), residues: 24 loop : -1.46 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP a5317 HIS 0.009 0.002 HIS b5201 PHE 0.024 0.002 PHE n 87 TYR 0.033 0.002 TYR m5026 ARG 0.005 0.000 ARG t5028 *********************** 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 898 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 712 time to evaluate : 3.930 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: A 226 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6178 (tm-30) REVERT: A 328 MET cc_start: 0.7836 (mmp) cc_final: 0.7636 (mtm) REVERT: B 24 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9053 (mm) REVERT: B 37 MET cc_start: 0.9332 (tpp) cc_final: 0.9118 (tpp) REVERT: B 317 ASN cc_start: 0.7396 (t0) cc_final: 0.6865 (t0) REVERT: B 410 THR cc_start: 0.7487 (m) cc_final: 0.7183 (p) REVERT: B 485 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.3762 (tp30) REVERT: C 243 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9148 (tt) REVERT: D 80 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7810 (p) REVERT: D 85 MET cc_start: 0.8426 (tmm) cc_final: 0.8087 (tmm) REVERT: D 126 MET cc_start: 0.8283 (tpp) cc_final: 0.7950 (tpp) REVERT: D 332 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7756 (mm-40) REVERT: I 1 MET cc_start: 0.6651 (mmm) cc_final: 0.6047 (mmp) REVERT: I 21 PHE cc_start: 0.8476 (m-10) cc_final: 0.8213 (m-80) REVERT: L 4 ASN cc_start: 0.7240 (t0) cc_final: 0.6872 (t0) REVERT: T 8 PHE cc_start: 0.8656 (t80) cc_final: 0.8267 (t80) REVERT: a 5064 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5459 (mtm180) REVERT: a 5112 TYR cc_start: 0.8676 (t80) cc_final: 0.8181 (t80) REVERT: a 5172 MET cc_start: 0.8905 (ttm) cc_final: 0.8597 (ttt) REVERT: a 5187 GLN cc_start: 0.9215 (tp40) cc_final: 0.8786 (tp-100) REVERT: a 5261 GLN cc_start: 0.6737 (tt0) cc_final: 0.6289 (pp30) REVERT: a 5319 ASP cc_start: 0.8221 (m-30) cc_final: 0.7891 (t0) REVERT: a 5332 HIS cc_start: 0.7999 (t-90) cc_final: 0.7753 (t70) REVERT: b 5188 ASP cc_start: 0.7943 (p0) cc_final: 0.7664 (p0) REVERT: d 5080 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7208 (t) REVERT: d 5126 MET cc_start: 0.8124 (tpp) cc_final: 0.7839 (tpp) REVERT: d 5210 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8522 (tt) REVERT: d 5213 ILE cc_start: 0.9191 (tp) cc_final: 0.8932 (tp) REVERT: d 5244 TYR cc_start: 0.8887 (p90) cc_final: 0.8664 (p90) REVERT: d 5333 ASP cc_start: 0.7807 (t70) cc_final: 0.7526 (t0) REVERT: i 5001 MET cc_start: 0.6082 (mmt) cc_final: 0.5175 (mmp) REVERT: i 5021 PHE cc_start: 0.8552 (m-10) cc_final: 0.8279 (m-80) REVERT: k 5038 VAL cc_start: 0.9252 (t) cc_final: 0.9031 (p) REVERT: l 5004 ASN cc_start: 0.6866 (t0) cc_final: 0.6634 (t0) REVERT: t 5006 TYR cc_start: 0.8485 (m-80) cc_final: 0.7918 (m-80) REVERT: Y 43 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.7996 (mmp-170) REVERT: n 107 ARG cc_start: 0.5585 (ttt90) cc_final: 0.5364 (ttt-90) REVERT: n 118 GLU cc_start: 0.6086 (tm-30) cc_final: 0.5884 (tm-30) REVERT: y 43 ARG cc_start: 0.8834 (mtp85) cc_final: 0.8282 (mmp-170) outliers start: 186 outliers final: 109 residues processed: 815 average time/residue: 0.4763 time to fit residues: 662.8381 Evaluate side-chains 747 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 631 time to evaluate : 4.231 ------------------------------------------------------------------------------- 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 286 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 159 ILE 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 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 5 THR 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 K residue 13 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 21 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 5030 VAL 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 5290 ILE Chi-restraints excluded: chain a residue 5300 PHE 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 5181 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5354 GLU Chi-restraints excluded: chain c residue 5396 MET Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5466 VAL Chi-restraints excluded: chain d residue 5019 ASP Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5057 SER Chi-restraints excluded: chain d residue 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5138 VAL Chi-restraints excluded: chain d residue 5159 ILE 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 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG 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 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 5035 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 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 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 n residue 68 LEU Chi-restraints excluded: chain y residue 39 LEU Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 25 PHE Chi-restraints excluded: chain X residue 36 LYS 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 373 optimal weight: 8.9990 chunk 283 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 378 optimal weight: 6.9990 chunk 401 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a5130 GLN ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c5229 ASN d5189 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42522 Z= 0.242 Angle : 0.765 13.016 58759 Z= 0.334 Chirality : 0.045 0.374 5783 Planarity : 0.005 0.064 7335 Dihedral : 18.139 174.976 8213 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 4.85 % Allowed : 16.78 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4240 helix: 0.51 (0.10), residues: 2357 sheet: -1.45 (1.00), residues: 24 loop : -1.37 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a5317 HIS 0.008 0.001 HIS F 24 PHE 0.027 0.002 PHE T 10 TYR 0.035 0.002 TYR A 112 ARG 0.005 0.000 ARG n 76 *********************** 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 862 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 696 time to evaluate : 3.698 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 226 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6377 (tm-30) REVERT: B 188 ASP cc_start: 0.7855 (p0) cc_final: 0.7595 (p0) REVERT: B 256 MET cc_start: 0.8227 (tpp) cc_final: 0.7793 (tpp) REVERT: B 317 ASN cc_start: 0.7484 (t0) cc_final: 0.6940 (t0) REVERT: B 330 MET cc_start: 0.8653 (mtp) cc_final: 0.8445 (mtp) REVERT: B 410 THR cc_start: 0.7552 (m) cc_final: 0.7205 (p) REVERT: C 243 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9163 (tt) REVERT: D 126 MET cc_start: 0.8214 (tpp) cc_final: 0.7836 (tpp) REVERT: D 295 SER cc_start: 0.8766 (t) cc_final: 0.8419 (p) REVERT: E 71 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7470 (mm-30) REVERT: I 1 MET cc_start: 0.6477 (mmm) cc_final: 0.5984 (mmp) REVERT: I 21 PHE cc_start: 0.8442 (m-10) cc_final: 0.8198 (m-80) REVERT: L 4 ASN cc_start: 0.7321 (t0) cc_final: 0.6967 (t0) REVERT: T 8 PHE cc_start: 0.8606 (t80) cc_final: 0.8333 (t80) REVERT: Z 27 TYR cc_start: 0.8079 (m-80) cc_final: 0.7861 (m-80) REVERT: a 5064 ARG cc_start: 0.6031 (mmm160) cc_final: 0.5475 (mtm180) REVERT: a 5112 TYR cc_start: 0.8670 (t80) cc_final: 0.8213 (t80) REVERT: a 5172 MET cc_start: 0.8962 (ttm) cc_final: 0.8695 (ttt) REVERT: a 5187 GLN cc_start: 0.9123 (tp40) cc_final: 0.8918 (tp-100) REVERT: a 5261 GLN cc_start: 0.6577 (tt0) cc_final: 0.6368 (pp30) REVERT: a 5319 ASP cc_start: 0.8220 (m-30) cc_final: 0.7882 (t0) REVERT: b 5410 THR cc_start: 0.7304 (m) cc_final: 0.7022 (p) REVERT: c 5342 MET cc_start: 0.6762 (tmm) cc_final: 0.6359 (tmm) REVERT: d 5098 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: d 5126 MET cc_start: 0.8240 (tpp) cc_final: 0.7917 (tpp) REVERT: d 5213 ILE cc_start: 0.9164 (tp) cc_final: 0.8889 (tp) REVERT: d 5244 TYR cc_start: 0.8819 (p90) cc_final: 0.8545 (p90) REVERT: f 5041 GLN cc_start: 0.6781 (tm-30) cc_final: 0.6541 (tm-30) REVERT: i 5001 MET cc_start: 0.6100 (mmt) cc_final: 0.5288 (mmp) REVERT: i 5021 PHE cc_start: 0.8615 (m-10) cc_final: 0.8355 (m-80) REVERT: k 5038 VAL cc_start: 0.9253 (t) cc_final: 0.9047 (p) REVERT: l 5004 ASN cc_start: 0.6901 (t0) cc_final: 0.6677 (t0) REVERT: Y 38 LEU cc_start: 0.9197 (mm) cc_final: 0.8775 (mt) REVERT: Y 43 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7954 (mmp-170) REVERT: N 118 GLU cc_start: 0.4710 (tm-30) cc_final: 0.4419 (tm-30) REVERT: y 43 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8286 (mmp-170) outliers start: 166 outliers final: 115 residues processed: 785 average time/residue: 0.4772 time to fit residues: 641.0697 Evaluate side-chains 756 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 639 time to evaluate : 3.574 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 286 THR 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 368 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 159 ILE 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 277 THR Chi-restraints excluded: chain D residue 281 MET 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 5 THR 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 I residue 24 LEU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 13 ILE Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5091 LEU Chi-restraints excluded: chain a residue 5132 GLU Chi-restraints excluded: chain a residue 5200 LEU Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5300 PHE Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5181 VAL Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR 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 5121 SER 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 5079 SER Chi-restraints excluded: chain d residue 5098 GLN Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5159 ILE Chi-restraints excluded: chain d residue 5205 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 d residue 5281 MET Chi-restraints excluded: chain e residue 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain e residue 5078 THR Chi-restraints excluded: chain f residue 5023 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain i residue 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5013 ASN Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5011 THR Chi-restraints excluded: chain m residue 5013 LEU Chi-restraints excluded: chain m residue 5031 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 5016 SER 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 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain N residue 128 LEU Chi-restraints excluded: chain y residue 39 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 334 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 342 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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** ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN D 263 ASN E 74 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c5385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k5040 GLN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m5032 GLN ** n 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 42522 Z= 0.319 Angle : 0.775 13.030 58759 Z= 0.342 Chirality : 0.046 0.400 5783 Planarity : 0.005 0.061 7335 Dihedral : 17.075 173.528 8202 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 6.04 % Allowed : 17.63 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4240 helix: 0.62 (0.10), residues: 2372 sheet: -1.27 (1.00), residues: 24 loop : -1.33 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 340 HIS 0.010 0.002 HIS b5201 PHE 0.029 0.002 PHE t5010 TYR 0.036 0.002 TYR A 112 ARG 0.007 0.000 ARG c5362 *********************** 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 881 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 674 time to evaluate : 3.705 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: B 188 ASP cc_start: 0.7880 (p0) cc_final: 0.7626 (p0) REVERT: B 410 THR cc_start: 0.7616 (m) cc_final: 0.7232 (p) REVERT: C 243 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9201 (tt) REVERT: D 80 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7332 (t) REVERT: D 126 MET cc_start: 0.8244 (tpp) cc_final: 0.7931 (tpp) REVERT: D 129 GLN cc_start: 0.8552 (mt0) cc_final: 0.8301 (tt0) REVERT: D 210 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8533 (tt) REVERT: D 224 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7444 (tm130) REVERT: D 295 SER cc_start: 0.8802 (t) cc_final: 0.8464 (p) REVERT: D 297 ASP cc_start: 0.7173 (t0) cc_final: 0.6962 (t0) REVERT: E 56 TYR cc_start: 0.6891 (m-80) cc_final: 0.6595 (m-80) REVERT: F 41 GLN cc_start: 0.8015 (mp10) cc_final: 0.7770 (mp10) REVERT: I 1 MET cc_start: 0.6495 (mmm) cc_final: 0.6075 (mmp) REVERT: I 21 PHE cc_start: 0.8517 (m-10) cc_final: 0.8212 (m-80) REVERT: M 15 VAL cc_start: 0.9459 (OUTLIER) cc_final: 0.9225 (t) REVERT: M 16 LEU cc_start: 0.8623 (mp) cc_final: 0.8240 (mp) REVERT: T 8 PHE cc_start: 0.8621 (t80) cc_final: 0.8301 (t80) REVERT: Z 27 TYR cc_start: 0.8075 (m-80) cc_final: 0.7816 (m-80) REVERT: a 5064 ARG cc_start: 0.6044 (mmm160) cc_final: 0.5665 (mtm180) REVERT: a 5112 TYR cc_start: 0.8739 (t80) cc_final: 0.8302 (t80) REVERT: a 5170 ASP cc_start: 0.8183 (m-30) cc_final: 0.7973 (m-30) REVERT: a 5187 GLN cc_start: 0.9159 (tp40) cc_final: 0.8903 (tp-100) REVERT: a 5261 GLN cc_start: 0.6560 (tt0) cc_final: 0.6164 (pp30) REVERT: a 5319 ASP cc_start: 0.8297 (m-30) cc_final: 0.7892 (t0) REVERT: b 5317 ASN cc_start: 0.7482 (t0) cc_final: 0.6885 (t0) REVERT: b 5410 THR cc_start: 0.7339 (m) cc_final: 0.7040 (p) REVERT: c 5342 MET cc_start: 0.6910 (tmm) cc_final: 0.6369 (tmm) REVERT: d 5080 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7334 (t) REVERT: d 5098 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8426 (mp10) REVERT: d 5126 MET cc_start: 0.8142 (tpp) cc_final: 0.7906 (tpp) REVERT: d 5213 ILE cc_start: 0.9220 (tp) cc_final: 0.8928 (tp) REVERT: d 5244 TYR cc_start: 0.8837 (p90) cc_final: 0.8581 (p90) REVERT: d 5295 SER cc_start: 0.8966 (t) cc_final: 0.8575 (p) REVERT: i 5001 MET cc_start: 0.6043 (mmt) cc_final: 0.5311 (mmp) REVERT: i 5021 PHE cc_start: 0.8639 (m-10) cc_final: 0.8395 (m-80) REVERT: l 5004 ASN cc_start: 0.6982 (t0) cc_final: 0.6776 (t0) REVERT: t 5006 TYR cc_start: 0.8587 (m-80) cc_final: 0.8272 (m-80) REVERT: z 5039 LEU cc_start: 0.8186 (tp) cc_final: 0.7924 (mt) REVERT: Y 43 ARG cc_start: 0.8392 (mtp-110) cc_final: 0.8036 (mmp-170) REVERT: n 91 GLN cc_start: 0.6879 (tp40) cc_final: 0.6272 (tm-30) REVERT: y 43 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8283 (mmp-170) outliers start: 207 outliers final: 153 residues processed: 783 average time/residue: 0.4944 time to fit residues: 667.0396 Evaluate side-chains 794 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 634 time to evaluate : 3.919 ------------------------------------------------------------------------------- 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 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 224 GLN Chi-restraints excluded: chain D residue 225 ASP 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 277 THR Chi-restraints excluded: chain D residue 281 MET Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 25 ILE 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 F residue 31 ILE 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 I residue 16 VAL Chi-restraints excluded: chain I residue 24 LEU 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 33 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 29 THR 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 44 SER Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 5030 VAL 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 5145 VAL Chi-restraints excluded: chain a residue 5200 LEU 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 5300 PHE Chi-restraints excluded: chain b residue 5024 LEU Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5181 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 5371 THR 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 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5121 SER Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5174 LEU Chi-restraints excluded: chain c residue 5229 ASN Chi-restraints excluded: chain c residue 5287 THR 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 d residue 5030 VAL Chi-restraints excluded: chain d residue 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5098 GLN 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 5147 SER Chi-restraints excluded: chain d residue 5159 ILE Chi-restraints excluded: chain d residue 5192 THR Chi-restraints excluded: chain d residue 5205 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 d residue 5281 MET Chi-restraints excluded: chain d residue 5286 VAL Chi-restraints excluded: chain e residue 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain e residue 5078 THR Chi-restraints excluded: chain f residue 5023 VAL Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain f residue 5031 ILE Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain h residue 5060 VAL Chi-restraints excluded: chain i residue 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5009 ILE Chi-restraints excluded: chain m residue 5011 THR 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 5016 SER Chi-restraints excluded: chain z residue 5025 VAL Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 124 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain y residue 39 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 134 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 91 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c5385 GLN d5263 ASN ** d5292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42522 Z= 0.273 Angle : 0.742 14.232 58759 Z= 0.327 Chirality : 0.045 0.394 5783 Planarity : 0.005 0.061 7335 Dihedral : 16.649 175.062 8202 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 5.60 % Allowed : 19.38 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4240 helix: 0.75 (0.10), residues: 2376 sheet: -1.08 (1.00), residues: 24 loop : -1.29 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 340 HIS 0.008 0.001 HIS B 201 PHE 0.028 0.001 PHE t5010 TYR 0.040 0.002 TYR A 112 ARG 0.006 0.000 ARG E 51 *********************** 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 867 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 675 time to evaluate : 4.054 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: B 188 ASP cc_start: 0.7838 (p0) cc_final: 0.7586 (p0) REVERT: B 292 LEU cc_start: 0.7045 (pp) cc_final: 0.6701 (mt) REVERT: B 410 THR cc_start: 0.7610 (m) cc_final: 0.7205 (p) REVERT: C 243 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9224 (tt) REVERT: D 80 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7471 (t) REVERT: D 126 MET cc_start: 0.8203 (tpp) cc_final: 0.7891 (tpp) REVERT: D 210 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8617 (tt) REVERT: D 295 SER cc_start: 0.8775 (t) cc_final: 0.8495 (p) REVERT: E 56 TYR cc_start: 0.7000 (m-80) cc_final: 0.6800 (m-80) REVERT: I 1 MET cc_start: 0.6629 (mmm) cc_final: 0.6320 (mmp) REVERT: I 21 PHE cc_start: 0.8480 (m-10) cc_final: 0.8159 (m-80) REVERT: T 8 PHE cc_start: 0.8613 (t80) cc_final: 0.8299 (t80) REVERT: Z 1 MET cc_start: 0.6916 (pmm) cc_final: 0.6314 (pmm) REVERT: a 5064 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5574 (mtm180) REVERT: a 5112 TYR cc_start: 0.8757 (t80) cc_final: 0.8394 (t80) REVERT: a 5317 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.7178 (m-10) REVERT: a 5319 ASP cc_start: 0.8295 (m-30) cc_final: 0.7960 (t0) REVERT: b 5145 LEU cc_start: 0.9363 (tt) cc_final: 0.9148 (mt) REVERT: b 5292 LEU cc_start: 0.7193 (pp) cc_final: 0.6870 (mt) REVERT: b 5317 ASN cc_start: 0.7591 (t0) cc_final: 0.7099 (t0) REVERT: b 5410 THR cc_start: 0.7425 (m) cc_final: 0.7149 (p) REVERT: c 5342 MET cc_start: 0.7167 (tmm) cc_final: 0.6463 (tmm) REVERT: d 5080 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7405 (t) REVERT: d 5098 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: d 5126 MET cc_start: 0.8138 (tpp) cc_final: 0.7864 (tpp) REVERT: d 5160 TYR cc_start: 0.9359 (t80) cc_final: 0.9089 (t80) REVERT: d 5244 TYR cc_start: 0.8855 (p90) cc_final: 0.8634 (p90) REVERT: d 5295 SER cc_start: 0.8997 (t) cc_final: 0.8688 (p) REVERT: i 5001 MET cc_start: 0.6128 (mmt) cc_final: 0.5331 (mmp) REVERT: i 5021 PHE cc_start: 0.8606 (m-10) cc_final: 0.8375 (m-80) REVERT: t 5006 TYR cc_start: 0.8581 (m-80) cc_final: 0.8228 (m-80) REVERT: z 5019 MET cc_start: 0.8453 (tmm) cc_final: 0.8077 (tmm) REVERT: Y 43 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8003 (mmp-170) REVERT: N 76 ARG cc_start: 0.5885 (tpt90) cc_final: 0.5625 (tpt170) REVERT: N 118 GLU cc_start: 0.5407 (tm-30) cc_final: 0.5062 (tm-30) REVERT: y 43 ARG cc_start: 0.8821 (mtp85) cc_final: 0.8254 (mmp-170) REVERT: X 12 ILE cc_start: 0.8809 (mt) cc_final: 0.8554 (tt) REVERT: X 14 LEU cc_start: 0.8080 (tt) cc_final: 0.7749 (pp) outliers start: 192 outliers final: 153 residues processed: 789 average time/residue: 0.4755 time to fit residues: 645.7197 Evaluate side-chains 797 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 637 time to evaluate : 4.029 ------------------------------------------------------------------------------- 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 132 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 214 MET 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 112 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 225 ASP 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 281 MET Chi-restraints excluded: chain D residue 286 VAL 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 F residue 31 ILE 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 I residue 16 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 14 ILE Chi-restraints excluded: chain Z residue 44 SER Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5018 CYS Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5047 CYS Chi-restraints excluded: chain a residue 5064 ARG 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 5184 ILE Chi-restraints excluded: chain a residue 5200 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 5290 ILE Chi-restraints excluded: chain a residue 5300 PHE Chi-restraints excluded: chain a residue 5317 TRP Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5181 VAL Chi-restraints excluded: chain b residue 5217 ILE Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5266 GLU Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5437 LEU Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5119 LEU Chi-restraints excluded: chain c residue 5121 SER Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5229 ASN Chi-restraints excluded: chain c residue 5287 THR Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5410 VAL 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 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5098 GLN 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 5159 ILE Chi-restraints excluded: chain d residue 5205 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 d residue 5281 MET Chi-restraints excluded: chain d residue 5286 VAL Chi-restraints excluded: chain e residue 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5070 PHE Chi-restraints excluded: chain e residue 5078 THR 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 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5013 ASN Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5009 ILE Chi-restraints excluded: chain m residue 5011 THR Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5013 ILE Chi-restraints excluded: chain t residue 5014 ILE Chi-restraints excluded: chain t residue 5017 PHE 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 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain y residue 39 LEU 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 387 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 293 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 399 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d5263 ASN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42522 Z= 0.199 Angle : 0.717 13.060 58759 Z= 0.318 Chirality : 0.044 0.426 5783 Planarity : 0.005 0.056 7335 Dihedral : 16.097 177.801 8202 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 4.96 % Allowed : 20.75 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4240 helix: 0.90 (0.10), residues: 2385 sheet: -1.00 (1.01), residues: 24 loop : -1.21 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a5317 HIS 0.006 0.001 HIS a5215 PHE 0.032 0.001 PHE t5010 TYR 0.041 0.002 TYR A 112 ARG 0.008 0.000 ARG E 51 *********************** 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 860 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 690 time to evaluate : 4.150 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: B 292 LEU cc_start: 0.6864 (pp) cc_final: 0.6663 (mt) REVERT: B 410 THR cc_start: 0.7547 (m) cc_final: 0.7312 (p) REVERT: C 243 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9272 (tt) REVERT: D 43 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8956 (mm) REVERT: D 80 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7476 (t) REVERT: D 126 MET cc_start: 0.8158 (tpp) cc_final: 0.7830 (tpp) REVERT: D 295 SER cc_start: 0.8776 (t) cc_final: 0.8541 (p) REVERT: D 297 ASP cc_start: 0.7014 (t0) cc_final: 0.6791 (t0) REVERT: I 1 MET cc_start: 0.6700 (mmm) cc_final: 0.6383 (mmp) REVERT: a 5064 ARG cc_start: 0.5939 (OUTLIER) cc_final: 0.5543 (mtm180) REVERT: a 5098 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6534 (tm-30) REVERT: a 5112 TYR cc_start: 0.8717 (t80) cc_final: 0.8333 (t80) REVERT: b 5256 MET cc_start: 0.8076 (tpp) cc_final: 0.7747 (tpp) REVERT: b 5410 THR cc_start: 0.7501 (m) cc_final: 0.7099 (p) REVERT: c 5282 MET cc_start: 0.8598 (mtm) cc_final: 0.7971 (mtm) REVERT: d 5080 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7380 (t) REVERT: d 5098 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: d 5126 MET cc_start: 0.8072 (tpp) cc_final: 0.7744 (tpp) REVERT: d 5220 ASN cc_start: 0.7967 (m-40) cc_final: 0.7497 (m-40) REVERT: d 5244 TYR cc_start: 0.8645 (p90) cc_final: 0.8210 (p90) REVERT: d 5295 SER cc_start: 0.9008 (t) cc_final: 0.8716 (p) REVERT: i 5001 MET cc_start: 0.6063 (mmt) cc_final: 0.5498 (mmp) REVERT: t 5006 TYR cc_start: 0.8636 (m-80) cc_final: 0.8397 (m-80) REVERT: z 5019 MET cc_start: 0.8399 (tmm) cc_final: 0.8019 (tmm) REVERT: z 5039 LEU cc_start: 0.8164 (tp) cc_final: 0.7930 (mt) REVERT: y 43 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8280 (mmp-170) REVERT: X 12 ILE cc_start: 0.8745 (mt) cc_final: 0.8505 (tt) REVERT: X 14 LEU cc_start: 0.8032 (tt) cc_final: 0.7723 (pp) outliers start: 170 outliers final: 136 residues processed: 796 average time/residue: 0.4736 time to fit residues: 652.8722 Evaluate side-chains 780 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 638 time to evaluate : 3.688 ------------------------------------------------------------------------------- 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 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 286 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 225 ASP 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 282 SER Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 18 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 I residue 24 LEU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 13 ASN 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 44 SER Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5041 LEU Chi-restraints excluded: chain a residue 5047 CYS Chi-restraints excluded: chain a residue 5064 ARG 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 5206 PHE Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5024 LEU Chi-restraints excluded: chain b residue 5055 MET Chi-restraints excluded: chain b residue 5102 VAL Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5181 VAL Chi-restraints excluded: chain b residue 5217 ILE Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5266 GLU Chi-restraints excluded: chain b residue 5365 SER Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5429 ILE Chi-restraints excluded: chain b residue 5437 LEU 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 5121 SER Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5229 ASN Chi-restraints excluded: chain c residue 5287 THR Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5410 VAL 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 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5098 GLN Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5114 ILE Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5138 VAL Chi-restraints excluded: chain d residue 5147 SER Chi-restraints excluded: chain d residue 5205 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 d residue 5323 GLU Chi-restraints excluded: chain e residue 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5078 THR Chi-restraints excluded: chain e residue 5080 LEU Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5048 ILE Chi-restraints excluded: chain i residue 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain k residue 5035 LEU Chi-restraints excluded: chain l residue 5013 ASN Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5009 ILE Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5013 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 5040 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain y residue 39 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 247 optimal weight: 0.4980 chunk 159 optimal weight: 10.0000 chunk 238 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 254 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 314 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 HIS ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b5281 GLN c5091 HIS ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e5082 GLN ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN N 69 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42522 Z= 0.182 Angle : 0.717 21.974 58759 Z= 0.316 Chirality : 0.044 0.420 5783 Planarity : 0.004 0.054 7335 Dihedral : 15.693 179.674 8202 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 4.50 % Allowed : 22.15 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4240 helix: 0.90 (0.10), residues: 2406 sheet: -0.90 (1.01), residues: 24 loop : -1.19 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP c5189 HIS 0.008 0.001 HIS D 189 PHE 0.029 0.001 PHE t5010 TYR 0.041 0.002 TYR A 112 ARG 0.009 0.000 ARG E 51 *********************** 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 833 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 679 time to evaluate : 3.976 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 126 TYR cc_start: 0.9118 (t80) cc_final: 0.8848 (t80) REVERT: A 317 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.6758 (m-10) REVERT: B 256 MET cc_start: 0.8103 (tpp) cc_final: 0.7662 (tpp) REVERT: B 292 LEU cc_start: 0.6991 (pp) cc_final: 0.6775 (mt) REVERT: B 410 THR cc_start: 0.7507 (m) cc_final: 0.7278 (p) REVERT: C 243 ILE cc_start: 0.9498 (mt) cc_final: 0.9268 (tt) REVERT: D 19 ASP cc_start: 0.8188 (t0) cc_final: 0.7942 (t70) REVERT: D 80 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7535 (t) REVERT: D 126 MET cc_start: 0.8118 (tpp) cc_final: 0.7798 (tpp) REVERT: D 127 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8734 (mm) REVERT: D 295 SER cc_start: 0.8794 (t) cc_final: 0.8561 (p) REVERT: D 297 ASP cc_start: 0.6862 (t0) cc_final: 0.6590 (t0) REVERT: I 1 MET cc_start: 0.6641 (mmm) cc_final: 0.6321 (mmp) REVERT: a 5064 ARG cc_start: 0.5907 (mmm160) cc_final: 0.5490 (mtm180) REVERT: a 5098 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6515 (tm-30) REVERT: a 5112 TYR cc_start: 0.8685 (t80) cc_final: 0.8350 (t80) REVERT: a 5200 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8840 (tt) REVERT: a 5224 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7720 (pt) REVERT: b 5256 MET cc_start: 0.8147 (tpp) cc_final: 0.7860 (tpp) REVERT: b 5276 ASP cc_start: 0.8204 (m-30) cc_final: 0.7926 (m-30) REVERT: b 5410 THR cc_start: 0.7471 (m) cc_final: 0.7075 (p) REVERT: c 5282 MET cc_start: 0.8594 (mtm) cc_final: 0.7959 (mtm) REVERT: d 5080 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7445 (t) REVERT: d 5098 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: d 5126 MET cc_start: 0.8062 (tpp) cc_final: 0.7739 (tpp) REVERT: d 5129 GLN cc_start: 0.9248 (mm-40) cc_final: 0.8969 (tp40) REVERT: d 5160 TYR cc_start: 0.9355 (t80) cc_final: 0.8834 (t80) REVERT: d 5244 TYR cc_start: 0.8622 (p90) cc_final: 0.8227 (p90) REVERT: d 5295 SER cc_start: 0.9067 (t) cc_final: 0.8852 (p) REVERT: i 5001 MET cc_start: 0.6039 (mmt) cc_final: 0.5661 (mmp) REVERT: i 5002 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6925 (tm-30) REVERT: z 5019 MET cc_start: 0.8393 (tmm) cc_final: 0.8013 (tmm) REVERT: z 5039 LEU cc_start: 0.8128 (tp) cc_final: 0.7840 (mt) REVERT: z 5057 LEU cc_start: 0.6487 (mp) cc_final: 0.5816 (mp) REVERT: Y 43 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.7782 (mmm160) REVERT: y 43 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8270 (mmp-170) REVERT: X 12 ILE cc_start: 0.8646 (mt) cc_final: 0.8431 (tt) REVERT: X 14 LEU cc_start: 0.8004 (tt) cc_final: 0.7711 (pp) outliers start: 154 outliers final: 114 residues processed: 775 average time/residue: 0.4785 time to fit residues: 638.1099 Evaluate side-chains 758 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 637 time to evaluate : 3.797 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 133 LEU 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 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 127 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 282 SER 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 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 K residue 13 GLU Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain Z residue 44 SER Chi-restraints excluded: chain a residue 5030 VAL 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 5200 LEU Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5224 ILE 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 5112 CYS Chi-restraints excluded: chain b residue 5181 VAL Chi-restraints excluded: chain b residue 5217 ILE Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5266 GLU Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5429 ILE Chi-restraints excluded: chain b residue 5437 LEU Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5238 ILE Chi-restraints excluded: chain c residue 5287 THR Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5366 LEU 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 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5098 GLN Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5147 SER Chi-restraints excluded: chain d residue 5205 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 d residue 5323 GLU Chi-restraints excluded: chain e residue 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5078 THR Chi-restraints excluded: chain e residue 5080 LEU Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain i residue 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain l residue 5013 ASN Chi-restraints excluded: chain l residue 5019 LEU Chi-restraints excluded: chain m residue 5009 ILE Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain t residue 5013 ILE Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain z residue 5050 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain n residue 50 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain N residue 68 LEU 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 363 optimal weight: 3.9990 chunk 383 optimal weight: 8.9990 chunk 349 optimal weight: 0.0040 chunk 372 optimal weight: 4.9990 chunk 224 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 352 optimal weight: 3.9990 chunk 371 optimal weight: 0.7980 overall best weight: 1.8796 ------------------------------------------------------------------------------- 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** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 58 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c5228 ASN ** d5129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 ASN ** N 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 42522 Z= 0.234 Angle : 0.746 26.055 58759 Z= 0.330 Chirality : 0.045 0.420 5783 Planarity : 0.005 0.184 7335 Dihedral : 15.617 177.136 8200 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 4.61 % Allowed : 22.88 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4240 helix: 0.91 (0.10), residues: 2411 sheet: -0.83 (1.02), residues: 24 loop : -1.17 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c5189 HIS 0.006 0.001 HIS D 189 PHE 0.033 0.001 PHE T 8 TYR 0.040 0.002 TYR A 112 ARG 0.058 0.001 ARG l5007 *********************** 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 809 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 651 time to evaluate : 4.102 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 183 MET cc_start: 0.8526 (mtt) cc_final: 0.8150 (mtt) REVERT: A 317 TRP cc_start: 0.8564 (OUTLIER) cc_final: 0.6841 (m-10) REVERT: B 276 ASP cc_start: 0.8201 (m-30) cc_final: 0.7946 (m-30) REVERT: B 292 LEU cc_start: 0.7062 (pp) cc_final: 0.6797 (mt) REVERT: B 410 THR cc_start: 0.7561 (m) cc_final: 0.7322 (p) REVERT: D 19 ASP cc_start: 0.8236 (t0) cc_final: 0.7971 (t70) REVERT: D 80 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7605 (t) REVERT: D 126 MET cc_start: 0.8229 (tpp) cc_final: 0.7889 (tpp) REVERT: D 295 SER cc_start: 0.8854 (t) cc_final: 0.8633 (p) REVERT: M 1 MET cc_start: 0.4982 (mmt) cc_final: 0.4549 (mmt) REVERT: a 5064 ARG cc_start: 0.5938 (mmm160) cc_final: 0.5495 (mtm180) REVERT: a 5098 GLU cc_start: 0.7028 (tm-30) cc_final: 0.6487 (tm-30) REVERT: a 5112 TYR cc_start: 0.8735 (t80) cc_final: 0.8453 (t80) REVERT: a 5224 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7655 (pt) REVERT: b 5410 THR cc_start: 0.7559 (m) cc_final: 0.7155 (p) REVERT: c 5180 MET cc_start: 0.7373 (mmp) cc_final: 0.7141 (mmm) REVERT: c 5282 MET cc_start: 0.8678 (mtm) cc_final: 0.8222 (mtp) REVERT: d 5080 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7432 (t) REVERT: d 5098 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: d 5126 MET cc_start: 0.8072 (tpp) cc_final: 0.7756 (tpp) REVERT: d 5160 TYR cc_start: 0.9386 (t80) cc_final: 0.8857 (t80) REVERT: d 5244 TYR cc_start: 0.8624 (p90) cc_final: 0.8202 (p90) REVERT: i 5001 MET cc_start: 0.6135 (mmt) cc_final: 0.5731 (mmp) REVERT: l 5004 ASN cc_start: 0.7330 (t0) cc_final: 0.7026 (t0) REVERT: z 5019 MET cc_start: 0.8389 (tmm) cc_final: 0.8004 (tmm) REVERT: Y 43 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7784 (mmm160) REVERT: N 95 ASN cc_start: 0.7332 (p0) cc_final: 0.7081 (p0) REVERT: y 43 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8292 (mmp-170) REVERT: X 12 ILE cc_start: 0.8659 (mt) cc_final: 0.8429 (tt) outliers start: 158 outliers final: 129 residues processed: 753 average time/residue: 0.5162 time to fit residues: 675.5889 Evaluate side-chains 771 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 637 time to evaluate : 3.830 ------------------------------------------------------------------------------- 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 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 290 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 217 ILE 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 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 125 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 265 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 VAL 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 60 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 15 TYR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain Z residue 44 SER Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5018 CYS Chi-restraints excluded: chain a residue 5030 VAL 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 5184 ILE Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5224 ILE Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5024 LEU Chi-restraints excluded: chain b residue 5055 MET Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5181 VAL Chi-restraints excluded: chain b residue 5217 ILE Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5266 GLU Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5437 LEU Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5229 ASN Chi-restraints excluded: chain c residue 5287 THR Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5366 LEU 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 5043 LEU Chi-restraints excluded: chain d residue 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5098 GLN Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5147 SER Chi-restraints excluded: chain d residue 5205 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 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5082 GLN Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain i residue 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain l residue 5013 ASN 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 5031 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain N residue 68 LEU 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 Chi-restraints excluded: chain x residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 244 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 413 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 254 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m5028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 119 GLN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 42522 Z= 0.352 Angle : 0.788 18.852 58759 Z= 0.352 Chirality : 0.046 0.432 5783 Planarity : 0.005 0.050 7335 Dihedral : 15.791 172.159 8200 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.67 % Rotamer: Outliers : 4.70 % Allowed : 23.09 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4240 helix: 0.82 (0.10), residues: 2417 sheet: -0.62 (1.05), residues: 24 loop : -1.23 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c5189 HIS 0.009 0.002 HIS B 201 PHE 0.027 0.002 PHE t5010 TYR 0.044 0.002 TYR A 112 ARG 0.010 0.001 ARG n 34 ********************** 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 800 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 639 time to evaluate : 4.512 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 183 MET cc_start: 0.8551 (mtt) cc_final: 0.8289 (mtt) REVERT: A 317 TRP cc_start: 0.8581 (OUTLIER) cc_final: 0.6818 (m-10) REVERT: B 256 MET cc_start: 0.8311 (tpp) cc_final: 0.7672 (tpt) REVERT: B 410 THR cc_start: 0.7741 (m) cc_final: 0.7489 (p) REVERT: C 49 LEU cc_start: 0.9233 (tp) cc_final: 0.9018 (tp) REVERT: D 126 MET cc_start: 0.8305 (tpp) cc_final: 0.7998 (tpp) REVERT: M 1 MET cc_start: 0.5177 (mmt) cc_final: 0.4747 (mmt) REVERT: a 5064 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5498 (mtm180) REVERT: a 5098 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6604 (tm-30) REVERT: a 5112 TYR cc_start: 0.8809 (t80) cc_final: 0.8541 (t80) REVERT: a 5224 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7671 (pt) REVERT: b 5256 MET cc_start: 0.8157 (tpp) cc_final: 0.7572 (tpt) REVERT: b 5410 THR cc_start: 0.7706 (m) cc_final: 0.7399 (p) REVERT: c 5218 PHE cc_start: 0.7629 (m-80) cc_final: 0.7383 (m-10) REVERT: c 5282 MET cc_start: 0.8782 (mtm) cc_final: 0.8160 (mtm) REVERT: d 5080 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7428 (t) REVERT: d 5098 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8383 (mt0) REVERT: d 5126 MET cc_start: 0.8072 (tpp) cc_final: 0.7777 (tpp) REVERT: d 5244 TYR cc_start: 0.8679 (p90) cc_final: 0.8288 (p90) REVERT: i 5001 MET cc_start: 0.6119 (mmt) cc_final: 0.5693 (mmp) REVERT: z 5019 MET cc_start: 0.8400 (tmm) cc_final: 0.8086 (tmm) REVERT: z 5039 LEU cc_start: 0.8062 (tp) cc_final: 0.7854 (mt) REVERT: z 5057 LEU cc_start: 0.6503 (mp) cc_final: 0.6264 (mt) REVERT: N 118 GLU cc_start: 0.5725 (tm-30) cc_final: 0.5373 (tm-30) REVERT: y 43 ARG cc_start: 0.8831 (mtp85) cc_final: 0.8184 (mmp-170) REVERT: X 12 ILE cc_start: 0.8912 (mt) cc_final: 0.8590 (tt) outliers start: 161 outliers final: 142 residues processed: 744 average time/residue: 0.4618 time to fit residues: 590.8635 Evaluate side-chains 761 residues out of total 3493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 614 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 ILE Chi-restraints excluded: chain A residue 317 TRP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 217 ILE 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 371 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 125 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 265 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 286 VAL 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 F residue 37 ILE Chi-restraints excluded: chain H residue 39 LEU 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 K residue 13 GLU Chi-restraints excluded: chain K residue 15 TYR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 13 LEU Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 44 SER Chi-restraints excluded: chain Z residue 52 LEU Chi-restraints excluded: chain a residue 5018 CYS Chi-restraints excluded: chain a residue 5030 VAL Chi-restraints excluded: chain a residue 5064 ARG 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 5184 ILE Chi-restraints excluded: chain a residue 5206 PHE Chi-restraints excluded: chain a residue 5210 LEU Chi-restraints excluded: chain a residue 5224 ILE Chi-restraints excluded: chain a residue 5288 LEU Chi-restraints excluded: chain a residue 5328 MET Chi-restraints excluded: chain b residue 5024 LEU Chi-restraints excluded: chain b residue 5055 MET Chi-restraints excluded: chain b residue 5112 CYS Chi-restraints excluded: chain b residue 5133 LEU Chi-restraints excluded: chain b residue 5181 VAL Chi-restraints excluded: chain b residue 5217 ILE Chi-restraints excluded: chain b residue 5246 PHE Chi-restraints excluded: chain b residue 5250 PHE Chi-restraints excluded: chain b residue 5266 GLU Chi-restraints excluded: chain b residue 5368 VAL Chi-restraints excluded: chain b residue 5371 THR Chi-restraints excluded: chain b residue 5399 VAL Chi-restraints excluded: chain b residue 5429 ILE Chi-restraints excluded: chain b residue 5437 LEU Chi-restraints excluded: chain b residue 5467 ILE Chi-restraints excluded: chain c residue 5033 PHE Chi-restraints excluded: chain c residue 5095 LEU Chi-restraints excluded: chain c residue 5167 VAL Chi-restraints excluded: chain c residue 5173 LEU Chi-restraints excluded: chain c residue 5228 ASN Chi-restraints excluded: chain c residue 5229 ASN Chi-restraints excluded: chain c residue 5238 ILE Chi-restraints excluded: chain c residue 5287 THR Chi-restraints excluded: chain c residue 5289 PHE Chi-restraints excluded: chain c residue 5366 LEU Chi-restraints excluded: chain c residue 5421 SER Chi-restraints excluded: chain c residue 5436 PHE Chi-restraints excluded: chain c residue 5472 LEU Chi-restraints excluded: chain d residue 5030 VAL Chi-restraints excluded: chain d residue 5043 LEU Chi-restraints excluded: chain d residue 5065 SER Chi-restraints excluded: chain d residue 5079 SER Chi-restraints excluded: chain d residue 5080 THR Chi-restraints excluded: chain d residue 5098 GLN Chi-restraints excluded: chain d residue 5107 LEU Chi-restraints excluded: chain d residue 5127 LEU Chi-restraints excluded: chain d residue 5147 SER Chi-restraints excluded: chain d residue 5205 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 5039 SER Chi-restraints excluded: chain e residue 5068 ASP Chi-restraints excluded: chain e residue 5069 ARG Chi-restraints excluded: chain e residue 5082 GLN Chi-restraints excluded: chain f residue 5028 VAL Chi-restraints excluded: chain h residue 5039 LEU Chi-restraints excluded: chain i residue 5004 LEU Chi-restraints excluded: chain i residue 5008 VAL Chi-restraints excluded: chain i residue 5024 LEU Chi-restraints excluded: chain l residue 5013 ASN 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 5031 SER Chi-restraints excluded: chain t residue 5003 THR Chi-restraints excluded: chain z residue 5012 LEU Chi-restraints excluded: chain z residue 5040 ILE Chi-restraints excluded: chain z residue 5050 LEU Chi-restraints excluded: chain Y residue 25 ILE Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain n residue 68 LEU Chi-restraints excluded: chain n residue 119 GLN Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU 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 Chi-restraints excluded: chain x residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 261 optimal weight: 8.9990 chunk 350 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 303 optimal weight: 0.0070 chunk 48 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 329 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 338 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a5190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5053 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b5058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d5142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e5074 GLN n 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.097250 restraints weight = 91641.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100647 restraints weight = 40145.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102874 restraints weight = 25426.737| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 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 = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42522 Z= 0.184 Angle : 0.755 20.529 58759 Z= 0.336 Chirality : 0.045 0.409 5783 Planarity : 0.005 0.051 7335 Dihedral : 15.407 166.343 8200 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 4.00 % Allowed : 23.82 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.13), residues: 4240 helix: 0.85 (0.10), residues: 2418 sheet: -0.63 (1.05), residues: 24 loop : -1.15 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 142 HIS 0.005 0.001 HIS D 189 PHE 0.034 0.001 PHE t5008 TYR 0.035 0.002 TYR A 112 ARG 0.010 0.000 ARG n 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10567.34 seconds wall clock time: 190 minutes 14.01 seconds (11414.01 seconds total)