Starting phenix.real_space_refine on Thu Mar 21 04:50:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c9r_30314/03_2024/7c9r_30314_updated.pdb" } resolution = 2.82 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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 17 9.91 5 Fe 5 7.16 5 P 25 5.49 5 Mg 37 5.21 5 S 156 5.16 5 C 20089 2.51 5 N 4062 2.21 5 O 4837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ARG 277": "NH1" <-> "NH2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 7": "OE1" <-> "OE2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "M GLU 3": "OE1" <-> "OE2" Residue "M PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 69": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M GLU 310": "OE1" <-> "OE2" Residue "H TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H GLU 169": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H GLU 255": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "J PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 44": "OD1" <-> "OD2" Residue "T PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 68": "OE1" <-> "OE2" Residue "Z PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "2 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 3": "OE1" <-> "OE2" Residue "4 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29228 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2433 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 285} Chain: "L" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2161 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain: "M" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2535 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 296} Chain: "H" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2017 Classifications: {'peptide': 257} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 236} Chain: "A" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 563 Classifications: {'peptide': 70} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 66} Chain: "B" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "D" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "G" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "I" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 588 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "K" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 580 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 588 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Chain: "P" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 628 Classifications: {'peptide': 78} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 71} Chain: "R" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "S" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 579 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain: "T" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "5" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 589 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "7" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 584 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "8" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "9" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 74} Chain: "0" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "C" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Unusual residues: {' CA': 1, ' MG': 1, 'DGA': 1, 'HEM': 4, 'PGV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'PGV:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 328 Unusual residues: {'8K6': 1, 'BCL': 2, 'BPH': 1, 'PGV': 1, 'UQ8': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UQ8:plan-6': 2, 'UQ8:plan-7': 2, 'UQ8:plan-8': 2, 'UQ8:plan-9': 2} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 290 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'MQ8': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PGV:plan-3': 1, 'PGV:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'H4X': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 204 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 319 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 2, 'PGV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 2, 'PGV:plan-2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 265 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 2, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 141 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "T" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 190 Unusual residues: {' CA': 1, 'BCL': 2, 'CDL': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 11 Chain: "Z" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 239 Unusual residues: {' CA': 1, '8K6': 1, 'BCL': 2, 'H4X': 1, 'PGV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "6" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'H4X': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {' CA': 1, 'BCL': 2, 'H4X': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {' CA': 1, 'BCL': 2, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "0" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" CB1 DGA C 407 " occ=0.70 ... (30 atoms not shown) pdb=" OA1 DGA C 407 " occ=0.70 Time building chain proxies: 15.73, per 1000 atoms: 0.54 Number of scatterers: 29228 At special positions: 0 Unit cell: (141.12, 126, 140.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 17 19.99 S 156 16.00 P 25 15.00 Mg 37 11.99 O 4837 8.00 N 4062 7.00 C 20089 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=42, symmetry=0 Number of additional bonds: simple=42, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.36 Conformation dependent library (CDL) restraints added in 4.0 seconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 6 sheets defined 57.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'C' and resid 46 through 55 removed outlier: 3.971A pdb=" N LYS C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 122 through 140 Processing helix chain 'C' and resid 226 through 243 removed outlier: 3.567A pdb=" N LEU C 243 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 264 through 282 Proline residue: C 268 - end of helix removed outlier: 3.731A pdb=" N ILE C 273 " --> pdb=" O TRP C 270 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C 282 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.845A pdb=" N GLU C 289 " --> pdb=" O PRO C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 33 through 55 Processing helix chain 'L' and resid 85 through 112 removed outlier: 3.661A pdb=" N VAL L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 133 removed outlier: 4.071A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 143 through 145 No H-bonds generated for 'chain 'L' and resid 143 through 145' Processing helix chain 'L' and resid 154 through 165 removed outlier: 4.381A pdb=" N THR L 165 " --> pdb=" O VAL L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 172 through 199 Processing helix chain 'L' and resid 210 through 220 removed outlier: 3.904A pdb=" N PHE L 217 " --> pdb=" O GLU L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 251 removed outlier: 4.454A pdb=" N HIS L 231 " --> pdb=" O ALA L 227 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 266 removed outlier: 4.088A pdb=" N TRP L 264 " --> pdb=" O TRP L 260 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET L 265 " --> pdb=" O PRO L 261 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP L 266 " --> pdb=" O GLU L 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 260 through 266' Processing helix chain 'M' and resid 38 through 43 removed outlier: 4.062A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 79 removed outlier: 4.673A pdb=" N LEU M 61 " --> pdb=" O GLY M 57 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL M 79 " --> pdb=" O MET M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 159 removed outlier: 3.794A pdb=" N ALA M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 180 through 192 Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.826A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 285 removed outlier: 3.936A pdb=" N CYS M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'H' and resid 12 through 23 Processing helix chain 'H' and resid 27 through 37 removed outlier: 4.010A pdb=" N LYS H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 216 through 219 removed outlier: 3.636A pdb=" N ASN H 219 " --> pdb=" O ILE H 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 216 through 219' Processing helix chain 'H' and resid 232 through 248 removed outlier: 3.829A pdb=" N GLY H 245 " --> pdb=" O TYR H 241 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 247 " --> pdb=" O GLY H 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 14 removed outlier: 4.438A pdb=" N HIS A 10 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 13 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 41 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.894A pdb=" N MET A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 42 Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 18 through 41 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 64 through 71 Processing helix chain 'E' and resid 11 through 42 Processing helix chain 'F' and resid 7 through 14 removed outlier: 4.526A pdb=" N HIS F 10 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP F 13 " --> pdb=" O HIS F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 41 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 64 through 71 Processing helix chain 'G' and resid 11 through 42 Processing helix chain 'I' and resid 8 through 14 removed outlier: 3.711A pdb=" N TRP I 13 " --> pdb=" O HIS I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 41 Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'I' and resid 64 through 71 Processing helix chain 'J' and resid 11 through 42 Processing helix chain 'K' and resid 8 through 14 removed outlier: 3.729A pdb=" N TRP K 13 " --> pdb=" O HIS K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 41 Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 64 through 71 Processing helix chain 'N' and resid 11 through 42 Processing helix chain 'O' and resid 9 through 14 removed outlier: 3.721A pdb=" N TRP O 13 " --> pdb=" O HIS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 41 Processing helix chain 'O' and resid 56 through 61 Processing helix chain 'O' and resid 64 through 71 Processing helix chain 'P' and resid 11 through 42 Processing helix chain 'Q' and resid 9 through 14 removed outlier: 3.699A pdb=" N TRP Q 13 " --> pdb=" O TYR Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 41 removed outlier: 3.644A pdb=" N SER Q 27 " --> pdb=" O LEU Q 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 42 Processing helix chain 'S' and resid 7 through 14 removed outlier: 4.398A pdb=" N HIS S 10 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP S 13 " --> pdb=" O HIS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 41 Processing helix chain 'S' and resid 56 through 61 Processing helix chain 'S' and resid 64 through 71 Processing helix chain 'T' and resid 11 through 42 Processing helix chain 'U' and resid 4 through 14 removed outlier: 3.804A pdb=" N ASP U 7 " --> pdb=" O LYS U 4 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY U 8 " --> pdb=" O SER U 5 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET U 9 " --> pdb=" O PHE U 6 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS U 10 " --> pdb=" O ASP U 7 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP U 13 " --> pdb=" O HIS U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 41 Processing helix chain 'U' and resid 56 through 61 Processing helix chain 'U' and resid 64 through 73 Processing helix chain 'V' and resid 11 through 42 Processing helix chain 'W' and resid 8 through 14 removed outlier: 3.736A pdb=" N TRP W 13 " --> pdb=" O HIS W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 41 Processing helix chain 'W' and resid 56 through 61 Processing helix chain 'W' and resid 64 through 71 Processing helix chain 'X' and resid 11 through 42 Processing helix chain 'Y' and resid 4 through 6 No H-bonds generated for 'chain 'Y' and resid 4 through 6' Processing helix chain 'Y' and resid 8 through 14 removed outlier: 3.724A pdb=" N TRP Y 13 " --> pdb=" O HIS Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 41 Processing helix chain 'Y' and resid 56 through 61 Processing helix chain 'Y' and resid 64 through 71 Processing helix chain 'Z' and resid 11 through 42 Processing helix chain '1' and resid 7 through 14 removed outlier: 4.180A pdb=" N HIS 1 10 " --> pdb=" O ASP 1 7 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP 1 13 " --> pdb=" O HIS 1 10 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 41 Processing helix chain '1' and resid 56 through 61 Processing helix chain '1' and resid 64 through 72 removed outlier: 3.624A pdb=" N ALA 1 72 " --> pdb=" O GLU 1 68 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 42 Processing helix chain '3' and resid 7 through 14 removed outlier: 4.352A pdb=" N HIS 3 10 " --> pdb=" O ASP 3 7 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP 3 13 " --> pdb=" O HIS 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 41 Processing helix chain '3' and resid 56 through 61 Processing helix chain '3' and resid 64 through 73 Processing helix chain '4' and resid 11 through 42 Processing helix chain '5' and resid 4 through 6 No H-bonds generated for 'chain '5' and resid 4 through 6' Processing helix chain '5' and resid 8 through 14 removed outlier: 3.758A pdb=" N TRP 5 13 " --> pdb=" O HIS 5 10 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 41 Processing helix chain '5' and resid 56 through 61 Processing helix chain '5' and resid 64 through 74 removed outlier: 3.692A pdb=" N LYS 5 74 " --> pdb=" O LYS 5 70 " (cutoff:3.500A) Processing helix chain '6' and resid 11 through 42 Processing helix chain '7' and resid 7 through 14 removed outlier: 4.508A pdb=" N HIS 7 10 " --> pdb=" O ASP 7 7 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP 7 13 " --> pdb=" O HIS 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 42 Processing helix chain '7' and resid 56 through 61 Processing helix chain '7' and resid 64 through 73 Processing helix chain '8' and resid 11 through 42 Processing helix chain '9' and resid 4 through 6 No H-bonds generated for 'chain '9' and resid 4 through 6' Processing helix chain '9' and resid 9 through 14 Processing helix chain '9' and resid 18 through 41 Processing helix chain '0' and resid 11 through 42 Processing sheet with id= A, first strand: chain 'C' and resid 29 through 32 Processing sheet with id= B, first strand: chain 'H' and resid 43 through 45 Processing sheet with id= C, first strand: chain 'H' and resid 64 through 67 Processing sheet with id= D, first strand: chain 'H' and resid 89 through 91 Processing sheet with id= E, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.794A pdb=" N GLU H 183 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR H 181 " --> pdb=" O ILE H 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 200 through 202 1233 hydrogen bonds defined for protein. 3504 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: 7.85 Time building geometry restraints manager: 12.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 7738 1.35 - 1.54: 20376 1.54 - 1.72: 1704 1.72 - 1.91: 300 1.91 - 2.10: 159 Bond restraints: 30277 Sorted by residual: bond pdb=" CZ ARG C 219 " pdb=" NH2 ARG C 219 " ideal model delta sigma weight residual 1.330 1.587 -0.257 1.30e-02 5.92e+03 3.90e+02 bond pdb=" NE ARG C 219 " pdb=" CZ ARG C 219 " ideal model delta sigma weight residual 1.326 1.480 -0.154 1.10e-02 8.26e+03 1.96e+02 bond pdb=" CZ TYR B 42 " pdb=" OH TYR B 42 " ideal model delta sigma weight residual 1.376 1.615 -0.239 2.10e-02 2.27e+03 1.30e+02 bond pdb=" C11 LMT P 102 " pdb=" C12 LMT P 102 " ideal model delta sigma weight residual 1.522 1.737 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C11 LMT T 102 " pdb=" C12 LMT T 102 " ideal model delta sigma weight residual 1.522 1.731 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 30272 not shown) Histogram of bond angle deviations from ideal: 81.84 - 101.32: 505 101.32 - 120.79: 31358 120.79 - 140.27: 9529 140.27 - 159.75: 38 159.75 - 179.23: 80 Bond angle restraints: 41510 Sorted by residual: angle pdb=" C34 H4X U 104 " pdb=" C33 H4X U 104 " pdb=" C35 H4X U 104 " ideal model delta sigma weight residual 74.50 125.20 -50.70 3.00e+00 1.11e-01 2.86e+02 angle pdb=" C24 H4X O 106 " pdb=" C23 H4X O 106 " pdb=" C25 H4X O 106 " ideal model delta sigma weight residual 74.52 123.65 -49.13 3.00e+00 1.11e-01 2.68e+02 angle pdb=" C24 H4X 6 101 " pdb=" C23 H4X 6 101 " pdb=" C25 H4X 6 101 " ideal model delta sigma weight residual 74.52 123.64 -49.12 3.00e+00 1.11e-01 2.68e+02 angle pdb=" C24 H4X K 103 " pdb=" C23 H4X K 103 " pdb=" C25 H4X K 103 " ideal model delta sigma weight residual 74.52 123.01 -48.49 3.00e+00 1.11e-01 2.61e+02 angle pdb=" C29 H4X G 101 " pdb=" C28 H4X G 101 " pdb=" C30 H4X G 101 " ideal model delta sigma weight residual 74.49 122.98 -48.49 3.00e+00 1.11e-01 2.61e+02 ... (remaining 41505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 16213 35.66 - 71.33: 995 71.33 - 106.99: 135 106.99 - 142.66: 65 142.66 - 178.32: 46 Dihedral angle restraints: 17454 sinusoidal: 8831 harmonic: 8623 Sorted by residual: dihedral pdb=" C1 BCL Q 103 " pdb=" CGA BCL Q 103 " pdb=" O2A BCL Q 103 " pdb=" CBA BCL Q 103 " ideal model delta sinusoidal sigma weight residual 180.00 93.04 86.96 1 6.00e+00 2.78e-02 2.53e+02 dihedral pdb=" C1 BCL 9 103 " pdb=" CGA BCL 9 103 " pdb=" O2A BCL 9 103 " pdb=" CBA BCL 9 103 " ideal model delta sinusoidal sigma weight residual 180.00 124.51 55.49 1 6.00e+00 2.78e-02 1.16e+02 dihedral pdb=" C1 BCL M 402 " pdb=" CGA BCL M 402 " pdb=" O2A BCL M 402 " pdb=" CBA BCL M 402 " ideal model delta sinusoidal sigma weight residual 180.00 129.78 50.22 1 6.00e+00 2.78e-02 9.61e+01 ... (remaining 17451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 3674 0.183 - 0.366: 497 0.366 - 0.549: 58 0.549 - 0.732: 6 0.732 - 0.915: 2 Chirality restraints: 4237 Sorted by residual: chirality pdb=" CA PHE H 3 " pdb=" N PHE H 3 " pdb=" C PHE H 3 " pdb=" CB PHE H 3 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CG LEU J 41 " pdb=" CB LEU J 41 " pdb=" CD1 LEU J 41 " pdb=" CD2 LEU J 41 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB VAL S 65 " pdb=" CA VAL S 65 " pdb=" CG1 VAL S 65 " pdb=" CG2 VAL S 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.63 2.00e-01 2.50e+01 9.95e+00 ... (remaining 4234 not shown) Planarity restraints: 4905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL Q 103 " -0.376 3.00e-02 1.11e+03 3.12e-01 5.42e+02 pdb=" CBA BCL Q 103 " -0.121 3.00e-02 1.11e+03 pdb=" CGA BCL Q 103 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL Q 103 " -0.140 3.00e-02 1.11e+03 pdb=" O2A BCL Q 103 " 0.552 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BPH M 404 " 0.223 2.00e-02 2.50e+03 1.86e-01 4.34e+02 pdb=" C2 BPH M 404 " -0.311 2.00e-02 2.50e+03 pdb=" C3 BPH M 404 " -0.060 2.00e-02 2.50e+03 pdb=" C4 BPH M 404 " 0.153 2.00e-02 2.50e+03 pdb=" C5 BPH M 404 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 9 103 " 0.318 3.00e-02 1.11e+03 2.56e-01 3.65e+02 pdb=" CBA BCL 9 103 " 0.196 3.00e-02 1.11e+03 pdb=" CGA BCL 9 103 " -0.088 3.00e-02 1.11e+03 pdb=" O1A BCL 9 103 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL 9 103 " -0.425 3.00e-02 1.11e+03 ... (remaining 4902 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 175 2.53 - 3.12: 19554 3.12 - 3.72: 41769 3.72 - 4.31: 67751 4.31 - 4.90: 111004 Nonbonded interactions: 240253 Sorted by model distance: nonbonded pdb=" CED BCL L 304 " pdb=" O1D BCL L 304 " model vdw 1.938 2.768 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.053 2.260 nonbonded pdb=" OD2 ASP H 93 " pdb=" NH1 ARG 9 19 " model vdw 2.098 2.520 nonbonded pdb=" O HIS 5 10 " pdb=" OG SER 6 14 " model vdw 2.142 2.440 nonbonded pdb=" O06 PGV 3 101 " pdb=" O12 PGV 3 101 " model vdw 2.164 2.440 ... (remaining 240248 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 '0' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '2' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '4' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '6' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain '8' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'B' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'E' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'G' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'J' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'N' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'P' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'R' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'T' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'V' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'X' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) selection = (chain 'Z' and (resid 7 through 11 or resid 13 or resid 15 through 19 or resid 2 \ 1 through 40 or resid 42 through 46)) } ncs_group { reference = (chain '1' and resid 3 through 72) selection = (chain '3' and resid 3 through 72) selection = (chain '5' and resid 3 through 72) selection = (chain '7' and resid 3 through 72) selection = (chain 'A' and resid 3 through 72) selection = (chain 'D' and resid 3 through 72) selection = (chain 'F' and resid 3 through 72) selection = (chain 'I' and resid 3 through 72) selection = (chain 'K' and resid 3 through 72) selection = (chain 'O' and resid 3 through 72) selection = (chain 'S' and resid 3 through 72) selection = (chain 'U' and resid 3 through 72) selection = (chain 'W' and resid 3 through 72) selection = (chain 'Y' and resid 3 through 72) } 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.370 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 71.540 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 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 : 0.020 0.257 30277 Z= 1.118 Angle : 3.324 50.704 41510 Z= 1.375 Chirality : 0.129 0.915 4237 Planarity : 0.019 0.312 4905 Dihedral : 24.651 178.321 11884 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 0.43 % Allowed : 4.53 % Favored : 95.04 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.57 (0.15), residues: 2937 helix: 0.58 (0.12), residues: 1713 sheet: -1.91 (0.66), residues: 55 loop : -1.76 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.015 TRP L 273 HIS 0.051 0.008 HIS D 37 PHE 0.084 0.012 PHE L 152 TYR 0.088 0.014 TYR B 42 ARG 0.125 0.004 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 432 time to evaluate : 2.839 Fit side-chains REVERT: L 200 ASN cc_start: 0.9305 (m-40) cc_final: 0.9013 (m110) REVERT: L 203 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8282 (ttpt) REVERT: M 135 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8248 (mtpt) REVERT: A 17 ASN cc_start: 0.9386 (t0) cc_final: 0.9135 (t0) REVERT: A 69 MET cc_start: 0.6981 (ttt) cc_final: 0.6529 (tmm) REVERT: G 22 MET cc_start: 0.9230 (mmt) cc_final: 0.8998 (mmm) REVERT: I 14 MET cc_start: 0.8986 (mtm) cc_final: 0.8753 (mtp) REVERT: K 4 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7424 (pmtt) REVERT: P 25 MET cc_start: 0.9187 (ttp) cc_final: 0.8960 (ttp) REVERT: S 69 MET cc_start: 0.5703 (mtt) cc_final: 0.5197 (ttp) REVERT: 5 69 MET cc_start: 0.8492 (mtt) cc_final: 0.8204 (mtm) outliers start: 11 outliers final: 4 residues processed: 442 average time/residue: 1.4308 time to fit residues: 739.3203 Evaluate side-chains 368 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 364 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 216 ILE Chi-restraints excluded: chain B residue 20 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 148 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 264 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 42 GLN C 50 GLN C 189 ASN C 215 ASN C 275 ASN L 145 HIS M 259 ASN H 42 GLN H 46 GLN O 29 GLN Q 29 GLN Y 29 GLN 7 2 ASN 7 29 GLN 7 59 GLN 9 86 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30277 Z= 0.179 Angle : 1.709 29.013 41510 Z= 0.587 Chirality : 0.043 0.333 4237 Planarity : 0.004 0.046 4905 Dihedral : 24.485 176.858 6411 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.87 % Allowed : 9.95 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.16 (0.16), residues: 2937 helix: 2.00 (0.13), residues: 1737 sheet: -1.41 (0.71), residues: 55 loop : -1.09 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 13 HIS 0.010 0.001 HIS L 154 PHE 0.019 0.001 PHE H 3 TYR 0.013 0.001 TYR H 85 ARG 0.005 0.000 ARG 9 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 381 time to evaluate : 2.849 Fit side-chains REVERT: C 114 THR cc_start: 0.8218 (p) cc_final: 0.8014 (m) REVERT: C 230 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: C 246 ASN cc_start: 0.8441 (m-40) cc_final: 0.8228 (m110) REVERT: L 200 ASN cc_start: 0.8916 (m-40) cc_final: 0.8654 (m110) REVERT: L 203 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8195 (ttpt) REVERT: L 213 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8954 (mt-10) REVERT: A 17 ASN cc_start: 0.9321 (t0) cc_final: 0.9074 (t0) REVERT: A 69 MET cc_start: 0.6972 (ttt) cc_final: 0.6506 (tmm) REVERT: K 4 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7328 (pmtt) REVERT: K 38 MET cc_start: 0.8780 (mmp) cc_final: 0.8493 (mmt) REVERT: S 69 MET cc_start: 0.5647 (mtt) cc_final: 0.5242 (ttp) REVERT: U 49 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.9058 (t0) REVERT: W 14 MET cc_start: 0.9055 (mtp) cc_final: 0.8776 (mtt) REVERT: 2 9 LEU cc_start: 0.8610 (mp) cc_final: 0.8369 (mt) REVERT: 4 15 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8301 (mtpp) outliers start: 48 outliers final: 13 residues processed: 407 average time/residue: 1.3711 time to fit residues: 655.7966 Evaluate side-chains 364 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 348 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain S residue 16 MET Chi-restraints excluded: chain U residue 49 ASP Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 264 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 235 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 145 HIS M 9 ASN W 59 GLN Y 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30277 Z= 0.310 Angle : 1.676 27.793 41510 Z= 0.586 Chirality : 0.050 0.439 4237 Planarity : 0.005 0.056 4905 Dihedral : 22.869 158.874 6407 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 10.97 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.48 (0.16), residues: 2937 helix: 2.19 (0.13), residues: 1720 sheet: -1.29 (0.73), residues: 55 loop : -0.78 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 92 HIS 0.011 0.001 HIS L 154 PHE 0.021 0.002 PHE H 3 TYR 0.013 0.002 TYR M 198 ARG 0.004 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 349 time to evaluate : 3.251 Fit side-chains REVERT: L 200 ASN cc_start: 0.9062 (m-40) cc_final: 0.8799 (m110) REVERT: L 203 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8168 (ttpt) REVERT: M 135 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7958 (mttt) REVERT: A 69 MET cc_start: 0.7225 (ttt) cc_final: 0.6645 (tmm) REVERT: E 22 MET cc_start: 0.8790 (mmm) cc_final: 0.8587 (mmm) REVERT: K 4 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7358 (pmtt) REVERT: K 38 MET cc_start: 0.8796 (mmt) cc_final: 0.8466 (mmt) REVERT: S 31 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7819 (t80) REVERT: S 69 MET cc_start: 0.5789 (mtt) cc_final: 0.5197 (ttp) REVERT: W 14 MET cc_start: 0.9105 (mtp) cc_final: 0.8801 (mtt) REVERT: 4 15 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (mtpp) outliers start: 55 outliers final: 24 residues processed: 376 average time/residue: 1.4103 time to fit residues: 619.9734 Evaluate side-chains 369 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 342 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 12 MET Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 3 residue 38 MET Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 8 residue 7 THR Chi-restraints excluded: chain 9 residue 77 SER Chi-restraints excluded: chain 0 residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 126 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 75 optimal weight: 0.0020 overall best weight: 1.1948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 HIS L 5 ASN H 42 GLN H 229 GLN H 252 ASN Y 29 GLN 9 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30277 Z= 0.175 Angle : 1.553 25.750 41510 Z= 0.535 Chirality : 0.045 0.413 4237 Planarity : 0.004 0.051 4905 Dihedral : 21.167 165.517 6407 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.80 % Allowed : 12.72 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.99 (0.16), residues: 2937 helix: 2.61 (0.13), residues: 1721 sheet: -1.24 (0.71), residues: 58 loop : -0.58 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 244 HIS 0.009 0.001 HIS L 154 PHE 0.016 0.001 PHE H 95 TYR 0.008 0.001 TYR M 193 ARG 0.003 0.000 ARG 9 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 353 time to evaluate : 2.738 Fit side-chains REVERT: C 230 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8766 (mt-10) REVERT: C 246 ASN cc_start: 0.8419 (m-40) cc_final: 0.8211 (m110) REVERT: L 200 ASN cc_start: 0.8800 (m-40) cc_final: 0.8547 (m110) REVERT: M 135 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: H 25 LEU cc_start: 0.8493 (tp) cc_final: 0.8144 (mp) REVERT: A 69 MET cc_start: 0.7219 (ttt) cc_final: 0.6651 (tmm) REVERT: B 15 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8334 (ttmt) REVERT: F 49 ASP cc_start: 0.9380 (m-30) cc_final: 0.8993 (m-30) REVERT: K 4 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7339 (pmtt) REVERT: K 38 MET cc_start: 0.8754 (mmt) cc_final: 0.8425 (mmt) REVERT: S 69 MET cc_start: 0.5818 (mtt) cc_final: 0.5274 (ttp) REVERT: W 14 MET cc_start: 0.9076 (mtp) cc_final: 0.8818 (mtt) REVERT: 2 9 LEU cc_start: 0.8535 (mp) cc_final: 0.8333 (mt) REVERT: 3 31 PHE cc_start: 0.8418 (m-10) cc_final: 0.7148 (t80) REVERT: 5 16 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8868 (ttp) REVERT: 9 73 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8931 (mm-30) outliers start: 46 outliers final: 17 residues processed: 375 average time/residue: 1.4018 time to fit residues: 616.6786 Evaluate side-chains 362 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 342 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 240 optimal weight: 0.1980 chunk 194 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN H 252 ASN Y 29 GLN 3 29 GLN 7 59 GLN ** 9 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 30277 Z= 0.424 Angle : 1.666 26.988 41510 Z= 0.588 Chirality : 0.053 0.505 4237 Planarity : 0.005 0.072 4905 Dihedral : 22.145 169.537 6407 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.26 % Allowed : 12.69 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.54 (0.16), residues: 2937 helix: 2.16 (0.12), residues: 1732 sheet: -1.25 (0.71), residues: 58 loop : -0.66 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 130 HIS 0.012 0.001 HIS L 154 PHE 0.020 0.002 PHE H 3 TYR 0.013 0.002 TYR M 198 ARG 0.004 0.001 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 340 time to evaluate : 3.006 Fit side-chains REVERT: L 200 ASN cc_start: 0.9130 (m-40) cc_final: 0.8870 (m110) REVERT: M 135 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7965 (mttt) REVERT: A 69 MET cc_start: 0.7235 (ttt) cc_final: 0.6606 (tmm) REVERT: F 49 ASP cc_start: 0.9427 (m-30) cc_final: 0.9046 (m-30) REVERT: K 4 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7379 (pmtt) REVERT: K 38 MET cc_start: 0.8821 (mmt) cc_final: 0.8512 (mmt) REVERT: O 38 MET cc_start: 0.9054 (tpt) cc_final: 0.8836 (tpt) REVERT: S 69 MET cc_start: 0.5991 (mtt) cc_final: 0.5376 (ttp) REVERT: 4 15 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8331 (mtpp) outliers start: 58 outliers final: 29 residues processed: 369 average time/residue: 1.4259 time to fit residues: 614.7448 Evaluate side-chains 362 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 331 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain L residue 38 SER Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.5980 chunk 253 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 233 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN C 246 ASN H 252 ASN Y 29 GLN 7 29 GLN 9 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30277 Z= 0.166 Angle : 1.538 26.809 41510 Z= 0.530 Chirality : 0.044 0.416 4237 Planarity : 0.004 0.055 4905 Dihedral : 20.873 178.197 6407 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.83 % Allowed : 13.47 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.05 (0.16), residues: 2937 helix: 2.61 (0.13), residues: 1734 sheet: -1.13 (0.70), residues: 58 loop : -0.51 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 13 HIS 0.009 0.001 HIS L 154 PHE 0.018 0.001 PHE 5 31 TYR 0.009 0.001 TYR M 193 ARG 0.002 0.000 ARG 9 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 335 time to evaluate : 3.128 Fit side-chains REVERT: L 200 ASN cc_start: 0.8785 (m-40) cc_final: 0.8542 (m110) REVERT: M 135 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7796 (mttt) REVERT: A 69 MET cc_start: 0.7234 (ttt) cc_final: 0.6580 (tmm) REVERT: E 22 MET cc_start: 0.8728 (mmm) cc_final: 0.8482 (mmm) REVERT: K 4 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7321 (pmtt) REVERT: K 38 MET cc_start: 0.8753 (mmt) cc_final: 0.8430 (mmt) REVERT: S 69 MET cc_start: 0.5925 (mtt) cc_final: 0.5346 (ttp) REVERT: W 14 MET cc_start: 0.9078 (mtp) cc_final: 0.8836 (mtt) REVERT: 3 31 PHE cc_start: 0.8426 (m-10) cc_final: 0.7171 (t80) outliers start: 47 outliers final: 25 residues processed: 365 average time/residue: 1.4071 time to fit residues: 601.4210 Evaluate side-chains 356 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 330 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 280 optimal weight: 0.4980 chunk 175 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 ASN H 42 GLN H 252 ASN Y 29 GLN 3 29 GLN 7 59 GLN 9 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30277 Z= 0.269 Angle : 1.580 26.757 41510 Z= 0.550 Chirality : 0.048 0.452 4237 Planarity : 0.005 0.059 4905 Dihedral : 21.064 168.696 6407 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.95 % Allowed : 13.86 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.92 (0.16), residues: 2937 helix: 2.46 (0.13), residues: 1738 sheet: -1.06 (0.70), residues: 58 loop : -0.50 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 13 HIS 0.011 0.001 HIS L 154 PHE 0.019 0.002 PHE 5 31 TYR 0.012 0.001 TYR M 198 ARG 0.002 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 335 time to evaluate : 3.061 Fit side-chains REVERT: L 200 ASN cc_start: 0.8963 (m-40) cc_final: 0.8712 (m110) REVERT: M 135 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7960 (mttt) REVERT: M 216 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8965 (t80) REVERT: A 69 MET cc_start: 0.7223 (ttt) cc_final: 0.6573 (tmm) REVERT: B 15 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8419 (ttmt) REVERT: E 22 MET cc_start: 0.8785 (mmm) cc_final: 0.8509 (mmm) REVERT: K 4 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7289 (pmtt) REVERT: K 38 MET cc_start: 0.8775 (mmt) cc_final: 0.8450 (mmt) REVERT: S 69 MET cc_start: 0.5957 (mtt) cc_final: 0.5344 (ttp) REVERT: W 14 MET cc_start: 0.9093 (mtp) cc_final: 0.8838 (mtt) REVERT: W 22 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8763 (mp) outliers start: 50 outliers final: 29 residues processed: 366 average time/residue: 1.4223 time to fit residues: 609.3264 Evaluate side-chains 365 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 332 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 3 residue 38 MET Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 ASN H 252 ASN Y 29 GLN 7 59 GLN 9 86 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30277 Z= 0.284 Angle : 1.590 26.784 41510 Z= 0.555 Chirality : 0.048 0.467 4237 Planarity : 0.005 0.064 4905 Dihedral : 21.136 159.326 6407 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.91 % Allowed : 13.93 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.82 (0.16), residues: 2937 helix: 2.38 (0.12), residues: 1738 sheet: -1.02 (0.70), residues: 58 loop : -0.54 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 130 HIS 0.012 0.001 HIS L 154 PHE 0.021 0.002 PHE 5 31 TYR 0.012 0.002 TYR M 198 ARG 0.002 0.000 ARG 6 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 335 time to evaluate : 3.005 Fit side-chains REVERT: L 200 ASN cc_start: 0.9012 (m-40) cc_final: 0.8764 (m110) REVERT: M 135 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7973 (mttt) REVERT: M 216 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8956 (t80) REVERT: A 69 MET cc_start: 0.7225 (ttt) cc_final: 0.6569 (tmm) REVERT: B 15 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8438 (ttmt) REVERT: K 4 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7293 (pmtt) REVERT: K 38 MET cc_start: 0.8793 (mmt) cc_final: 0.8472 (mmt) REVERT: S 31 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7781 (t80) REVERT: S 69 MET cc_start: 0.5882 (mtt) cc_final: 0.5287 (ttp) REVERT: W 14 MET cc_start: 0.9133 (mtp) cc_final: 0.8871 (mtt) REVERT: W 22 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8756 (mp) outliers start: 49 outliers final: 31 residues processed: 367 average time/residue: 1.4172 time to fit residues: 607.9204 Evaluate side-chains 370 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 334 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 3 residue 38 MET Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 49 ASN Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 3.9990 chunk 268 optimal weight: 0.3980 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 260 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 42 GLN H 252 ASN Y 29 GLN 7 29 GLN 7 59 GLN 9 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30277 Z= 0.180 Angle : 1.528 26.492 41510 Z= 0.527 Chirality : 0.044 0.415 4237 Planarity : 0.004 0.062 4905 Dihedral : 20.509 161.706 6407 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.44 % Allowed : 14.68 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 2.17 (0.16), residues: 2937 helix: 2.66 (0.13), residues: 1737 sheet: -0.96 (0.69), residues: 58 loop : -0.39 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 13 HIS 0.010 0.001 HIS L 154 PHE 0.020 0.001 PHE 5 31 TYR 0.008 0.001 TYR M 193 ARG 0.002 0.000 ARG 9 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 331 time to evaluate : 2.614 Fit side-chains REVERT: L 200 ASN cc_start: 0.8777 (m-40) cc_final: 0.8532 (m110) REVERT: M 135 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7837 (mttt) REVERT: M 216 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8772 (t80) REVERT: A 69 MET cc_start: 0.7200 (ttt) cc_final: 0.6542 (tmm) REVERT: E 22 MET cc_start: 0.8727 (mmm) cc_final: 0.8488 (mmm) REVERT: K 4 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7251 (pmtt) REVERT: K 38 MET cc_start: 0.8741 (mmt) cc_final: 0.8435 (mmt) REVERT: S 69 MET cc_start: 0.6014 (mtt) cc_final: 0.5411 (ttp) REVERT: W 14 MET cc_start: 0.9077 (mtp) cc_final: 0.8846 (mtt) REVERT: W 22 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8724 (mp) REVERT: 3 31 PHE cc_start: 0.8410 (m-10) cc_final: 0.7160 (t80) outliers start: 37 outliers final: 28 residues processed: 355 average time/residue: 1.4246 time to fit residues: 593.1327 Evaluate side-chains 361 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 330 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 196 PHE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain W residue 16 MET Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain 2 residue 39 SER Chi-restraints excluded: chain 3 residue 38 MET Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 ASN 3 29 GLN 5 29 GLN 7 2 ASN 7 59 GLN ** 9 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 30277 Z= 0.555 Angle : 1.718 27.676 41510 Z= 0.614 Chirality : 0.058 0.569 4237 Planarity : 0.006 0.091 4905 Dihedral : 21.987 166.418 6407 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.52 % Allowed : 14.60 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.30 (0.16), residues: 2937 helix: 1.91 (0.12), residues: 1744 sheet: -1.10 (0.71), residues: 58 loop : -0.69 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 130 HIS 0.013 0.001 HIS L 154 PHE 0.022 0.003 PHE H 3 TYR 0.020 0.003 TYR L 170 ARG 0.006 0.001 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 336 time to evaluate : 2.886 Fit side-chains REVERT: L 200 ASN cc_start: 0.9175 (m-40) cc_final: 0.8939 (m110) REVERT: M 135 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8011 (mttt) REVERT: A 69 MET cc_start: 0.7201 (ttt) cc_final: 0.6527 (tmm) REVERT: K 4 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7303 (pmtt) REVERT: K 38 MET cc_start: 0.8842 (mmt) cc_final: 0.8558 (mmt) REVERT: S 31 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7802 (t80) REVERT: S 69 MET cc_start: 0.6023 (mtt) cc_final: 0.5404 (ttp) outliers start: 39 outliers final: 25 residues processed: 361 average time/residue: 1.4585 time to fit residues: 613.7615 Evaluate side-chains 354 residues out of total 2570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 327 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 22 GLU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 20 LEU Chi-restraints excluded: chain Q residue 68 ASP Chi-restraints excluded: chain S residue 31 PHE Chi-restraints excluded: chain U residue 5 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain Y residue 5 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 61 GLU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 22 LEU Chi-restraints excluded: chain 4 residue 10 THR Chi-restraints excluded: chain 7 residue 5 SER Chi-restraints excluded: chain 9 residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 ASN 7 29 GLN 7 59 GLN 9 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.089517 restraints weight = 35520.218| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.14 r_work: 0.2737 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30277 Z= 0.171 Angle : 1.542 26.623 41510 Z= 0.533 Chirality : 0.045 0.446 4237 Planarity : 0.004 0.063 4905 Dihedral : 20.874 174.376 6407 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.09 % Allowed : 15.22 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.98 (0.16), residues: 2937 helix: 2.51 (0.13), residues: 1735 sheet: -0.94 (0.70), residues: 58 loop : -0.47 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 13 HIS 0.011 0.001 HIS L 154 PHE 0.021 0.001 PHE 5 31 TYR 0.009 0.001 TYR M 193 ARG 0.002 0.000 ARG M 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9969.05 seconds wall clock time: 176 minutes 57.26 seconds (10617.26 seconds total)