Starting phenix.real_space_refine on Wed Mar 20 09:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhe_42278/03_2024/8uhe_42278_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhe_42278/03_2024/8uhe_42278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhe_42278/03_2024/8uhe_42278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhe_42278/03_2024/8uhe_42278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhe_42278/03_2024/8uhe_42278_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uhe_42278/03_2024/8uhe_42278_updated.pdb" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 162 5.16 5 Cl 1 4.86 5 C 17061 2.51 5 N 4620 2.21 5 O 5204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E ASP 142": "OD1" <-> "OD2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "H ASP 64": "OD1" <-> "OD2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I GLU 132": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "J PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K ASP 382": "OD1" <-> "OD2" Residue "K TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 416": "OE1" <-> "OE2" Residue "K TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 507": "OE1" <-> "OE2" Residue "K GLU 543": "OE1" <-> "OE2" Residue "K GLU 568": "OE1" <-> "OE2" Residue "K GLU 622": "OE1" <-> "OE2" Residue "K GLU 660": "OE1" <-> "OE2" Residue "L ASP 13": "OD1" <-> "OD2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L ASP 64": "OD1" <-> "OD2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 114": "OE1" <-> "OE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M GLU 102": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "P TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 35": "OD1" <-> "OD2" Residue "P TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 100": "OD1" <-> "OD2" Residue "P TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "Q GLU 117": "OE1" <-> "OE2" Residue "R ASP 3": "OD1" <-> "OD2" Residue "R ASP 35": "OD1" <-> "OD2" Residue "R TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 54": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1300 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "F" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1214 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "H" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1246 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "J" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1311 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 4727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4727 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 30, 'TRANS': 562} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1207 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 2, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "N" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "P" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1222 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 158} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1233 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "R" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1214 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 157} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'M1V': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'M1V': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.83, per 1000 atoms: 0.55 Number of scatterers: 27048 At special positions: 0 Unit cell: (122.1, 123.75, 131.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 162 16.00 O 5204 8.00 N 4620 7.00 C 17061 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 4.7 seconds 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 163 helices and 2 sheets defined 71.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 20 through 29 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 47 through 61 Processing helix chain 'A' and resid 72 through 95 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 156 removed outlier: 4.259A pdb=" N TYR A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 21 through 46 removed outlier: 4.995A pdb=" N ASP B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 76 through 98 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 123 through 141 Processing helix chain 'B' and resid 144 through 160 removed outlier: 3.806A pdb=" N TYR B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 33 through 61 Proline residue: C 48 - end of helix Processing helix chain 'C' and resid 72 through 95 Processing helix chain 'C' and resid 99 through 102 No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 109 through 116 Processing helix chain 'C' and resid 120 through 137 Processing helix chain 'C' and resid 143 through 156 Proline residue: C 148 - end of helix removed outlier: 3.824A pdb=" N GLU C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.976A pdb=" N GLN D 15 " --> pdb=" O THR D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 59 removed outlier: 4.601A pdb=" N ASP D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 109 through 119 removed outlier: 4.497A pdb=" N LYS D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 141 Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.152A pdb=" N TYR D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 33 through 61 removed outlier: 5.873A pdb=" N GLU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 72 through 95 Processing helix chain 'E' and resid 99 through 102 No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 120 through 137 Processing helix chain 'E' and resid 140 through 156 removed outlier: 3.879A pdb=" N TYR E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 14 Processing helix chain 'F' and resid 21 through 46 removed outlier: 4.821A pdb=" N ASP F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 75 through 98 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 112 through 118 Processing helix chain 'F' and resid 123 through 141 Processing helix chain 'F' and resid 144 through 160 removed outlier: 3.790A pdb=" N TYR F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 20 through 61 removed outlier: 5.053A pdb=" N GLU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLN G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLU G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 72 through 95 Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 109 through 115 Processing helix chain 'G' and resid 120 through 137 Processing helix chain 'G' and resid 140 through 156 removed outlier: 3.747A pdb=" N TYR G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 21 through 46 removed outlier: 5.145A pdb=" N ASP H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 59 Processing helix chain 'H' and resid 76 through 98 Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 112 through 119 Processing helix chain 'H' and resid 123 through 141 removed outlier: 3.711A pdb=" N MET H 140 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 141 " --> pdb=" O VAL H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 160 removed outlier: 4.434A pdb=" N TYR H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 Processing helix chain 'I' and resid 20 through 61 Proline residue: I 34 - end of helix removed outlier: 5.416A pdb=" N GLU I 48 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 95 Processing helix chain 'I' and resid 99 through 104 Processing helix chain 'I' and resid 109 through 115 Processing helix chain 'I' and resid 120 through 136 Processing helix chain 'I' and resid 140 through 155 Proline residue: I 148 - end of helix Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 21 through 62 removed outlier: 4.485A pdb=" N ALA J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA J 49 " --> pdb=" O SER J 45 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 108 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 124 through 145 Processing helix chain 'J' and resid 152 through 164 Proline residue: J 156 - end of helix Processing helix chain 'K' and resid 20 through 30 Processing helix chain 'K' and resid 37 through 62 removed outlier: 4.578A pdb=" N LEU K 51 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLN K 52 " --> pdb=" O ARG K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 154 through 157 No H-bonds generated for 'chain 'K' and resid 154 through 157' Processing helix chain 'K' and resid 159 through 182 Processing helix chain 'K' and resid 186 through 192 Processing helix chain 'K' and resid 204 through 220 Processing helix chain 'K' and resid 229 through 243 Processing helix chain 'K' and resid 267 through 272 Processing helix chain 'K' and resid 287 through 301 Processing helix chain 'K' and resid 315 through 322 Processing helix chain 'K' and resid 328 through 336 Processing helix chain 'K' and resid 339 through 345 Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 370 through 393 removed outlier: 8.100A pdb=" N PHE K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER K 386 " --> pdb=" O ASP K 382 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA K 387 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 388 " --> pdb=" O GLY K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 401 Processing helix chain 'K' and resid 423 through 430 Processing helix chain 'K' and resid 441 through 450 removed outlier: 3.956A pdb=" N ARG K 450 " --> pdb=" O PHE K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 463 No H-bonds generated for 'chain 'K' and resid 461 through 463' Processing helix chain 'K' and resid 542 through 553 Processing helix chain 'K' and resid 560 through 562 No H-bonds generated for 'chain 'K' and resid 560 through 562' Processing helix chain 'K' and resid 565 through 572 Processing helix chain 'K' and resid 578 through 586 Processing helix chain 'K' and resid 589 through 595 Processing helix chain 'K' and resid 601 through 613 Processing helix chain 'K' and resid 620 through 632 Processing helix chain 'K' and resid 635 through 643 Processing helix chain 'K' and resid 646 through 651 Processing helix chain 'K' and resid 665 through 670 Processing helix chain 'L' and resid 4 through 15 Processing helix chain 'L' and resid 21 through 46 removed outlier: 4.661A pdb=" N ASP L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 59 Processing helix chain 'L' and resid 76 through 98 Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 112 through 119 Processing helix chain 'L' and resid 123 through 141 Processing helix chain 'L' and resid 143 through 159 removed outlier: 4.243A pdb=" N TYR L 152 " --> pdb=" O GLU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 11 Processing helix chain 'M' and resid 20 through 45 removed outlier: 5.335A pdb=" N GLU M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLN M 35 " --> pdb=" O LYS M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 61 Processing helix chain 'M' and resid 66 through 68 No H-bonds generated for 'chain 'M' and resid 66 through 68' Processing helix chain 'M' and resid 72 through 95 Processing helix chain 'M' and resid 99 through 105 Processing helix chain 'M' and resid 109 through 115 Processing helix chain 'M' and resid 120 through 136 Processing helix chain 'M' and resid 140 through 156 removed outlier: 4.043A pdb=" N TYR M 149 " --> pdb=" O GLU M 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 15 Processing helix chain 'N' and resid 21 through 46 removed outlier: 5.597A pdb=" N ASP N 35 " --> pdb=" O PHE N 31 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU N 36 " --> pdb=" O ARG N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 59 Processing helix chain 'N' and resid 76 through 98 Processing helix chain 'N' and resid 102 through 107 Processing helix chain 'N' and resid 112 through 119 Processing helix chain 'N' and resid 123 through 141 removed outlier: 3.845A pdb=" N MET N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 160 removed outlier: 3.842A pdb=" N TYR N 152 " --> pdb=" O GLU N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 11 Processing helix chain 'O' and resid 20 through 61 removed outlier: 5.048A pdb=" N GLU O 34 " --> pdb=" O VAL O 30 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN O 35 " --> pdb=" O LYS O 31 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLU O 48 " --> pdb=" O ALA O 44 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 95 Processing helix chain 'O' and resid 99 through 105 Processing helix chain 'O' and resid 109 through 115 Processing helix chain 'O' and resid 120 through 137 Processing helix chain 'O' and resid 140 through 156 removed outlier: 4.057A pdb=" N TYR O 149 " --> pdb=" O GLU O 145 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 15 removed outlier: 3.577A pdb=" N GLN P 15 " --> pdb=" O THR P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 59 removed outlier: 5.145A pdb=" N ASP P 35 " --> pdb=" O PHE P 31 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N SER P 49 " --> pdb=" O SER P 45 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 98 Processing helix chain 'P' and resid 102 through 107 Processing helix chain 'P' and resid 112 through 118 Processing helix chain 'P' and resid 123 through 141 Processing helix chain 'P' and resid 144 through 160 removed outlier: 4.111A pdb=" N TYR P 152 " --> pdb=" O GLU P 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 11 Processing helix chain 'Q' and resid 20 through 61 removed outlier: 5.137A pdb=" N GLU Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLU Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 95 Processing helix chain 'Q' and resid 99 through 104 Processing helix chain 'Q' and resid 109 through 115 Processing helix chain 'Q' and resid 120 through 137 Processing helix chain 'Q' and resid 140 through 156 removed outlier: 3.908A pdb=" N TYR Q 149 " --> pdb=" O GLU Q 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 15 removed outlier: 3.770A pdb=" N GLN R 15 " --> pdb=" O THR R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 46 removed outlier: 5.776A pdb=" N ASP R 35 " --> pdb=" O PHE R 31 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU R 36 " --> pdb=" O ARG R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 59 Processing helix chain 'R' and resid 76 through 98 Processing helix chain 'R' and resid 102 through 107 Processing helix chain 'R' and resid 112 through 119 Processing helix chain 'R' and resid 123 through 160 removed outlier: 6.195A pdb=" N ALA R 143 " --> pdb=" O ASP R 139 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N GLU R 144 " --> pdb=" O MET R 140 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU R 148 " --> pdb=" O GLU R 144 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL R 149 " --> pdb=" O ALA R 145 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR R 152 " --> pdb=" O GLU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 45 removed outlier: 4.312A pdb=" N PHE S 37 " --> pdb=" O TYR S 33 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 251 through 253 Processing sheet with id= B, first strand: chain 'S' and resid 26 through 32 removed outlier: 7.266A pdb=" N CYS S 9 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE S 50 " --> pdb=" O CYS S 9 " (cutoff:3.500A) 1696 hydrogen bonds defined for protein. 5082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 12.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.23: 252 1.23 - 1.39: 10590 1.39 - 1.54: 16219 1.54 - 1.70: 205 1.70 - 1.86: 256 Bond restraints: 27522 Sorted by residual: bond pdb=" CG PRO Q 66 " pdb=" CD PRO Q 66 " ideal model delta sigma weight residual 1.503 1.141 0.362 3.40e-02 8.65e+02 1.13e+02 bond pdb=" CG1 ILE I 4 " pdb=" CD1 ILE I 4 " ideal model delta sigma weight residual 1.513 1.124 0.389 3.90e-02 6.57e+02 9.96e+01 bond pdb=" CD GLU L 29 " pdb=" OE1 GLU L 29 " ideal model delta sigma weight residual 1.249 1.072 0.177 1.90e-02 2.77e+03 8.69e+01 bond pdb=" CG1 ILE M 25 " pdb=" CD1 ILE M 25 " ideal model delta sigma weight residual 1.513 1.163 0.350 3.90e-02 6.57e+02 8.04e+01 bond pdb=" CD GLU L 144 " pdb=" OE2 GLU L 144 " ideal model delta sigma weight residual 1.249 1.088 0.161 1.90e-02 2.77e+03 7.18e+01 ... (remaining 27517 not shown) Histogram of bond angle deviations from ideal: 88.11 - 100.40: 63 100.40 - 112.68: 14207 112.68 - 124.97: 22256 124.97 - 137.26: 747 137.26 - 149.54: 25 Bond angle restraints: 37298 Sorted by residual: angle pdb=" CA PRO Q 66 " pdb=" N PRO Q 66 " pdb=" CD PRO Q 66 " ideal model delta sigma weight residual 112.00 93.51 18.49 1.40e+00 5.10e-01 1.75e+02 angle pdb=" N SER C 163 " pdb=" CA SER C 163 " pdb=" C SER C 163 " ideal model delta sigma weight residual 109.96 125.85 -15.89 1.49e+00 4.50e-01 1.14e+02 angle pdb=" N PRO Q 66 " pdb=" CD PRO Q 66 " pdb=" CG PRO Q 66 " ideal model delta sigma weight residual 103.20 88.11 15.09 1.50e+00 4.44e-01 1.01e+02 angle pdb=" CA LEU C 157 " pdb=" C LEU C 157 " pdb=" O LEU C 157 " ideal model delta sigma weight residual 119.51 129.65 -10.14 1.04e+00 9.25e-01 9.51e+01 angle pdb=" CA PRO C 63 " pdb=" N PRO C 63 " pdb=" CD PRO C 63 " ideal model delta sigma weight residual 112.00 101.17 10.83 1.40e+00 5.10e-01 5.99e+01 ... (remaining 37293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 14862 22.02 - 44.04: 1679 44.04 - 66.05: 355 66.05 - 88.07: 90 88.07 - 110.09: 12 Dihedral angle restraints: 16998 sinusoidal: 7201 harmonic: 9797 Sorted by residual: dihedral pdb=" CA MET K 694 " pdb=" C MET K 694 " pdb=" N ARG K 695 " pdb=" CA ARG K 695 " ideal model delta harmonic sigma weight residual -180.00 -146.72 -33.28 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA THR B 74 " pdb=" C THR B 74 " pdb=" N CYS B 75 " pdb=" CA CYS B 75 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ARG L 32 " pdb=" C ARG L 32 " pdb=" N SER L 33 " pdb=" CA SER L 33 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 16995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4052 0.204 - 0.408: 41 0.408 - 0.612: 2 0.612 - 0.816: 0 0.816 - 1.020: 1 Chirality restraints: 4096 Sorted by residual: chirality pdb=" CG LEU L 36 " pdb=" CB LEU L 36 " pdb=" CD1 LEU L 36 " pdb=" CD2 LEU L 36 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA ARG C 159 " pdb=" N ARG C 159 " pdb=" C ARG C 159 " pdb=" CB ARG C 159 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CB THR F 55 " pdb=" CA THR F 55 " pdb=" OG1 THR F 55 " pdb=" CG2 THR F 55 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.89e+00 ... (remaining 4093 not shown) Planarity restraints: 4812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A M1V K 801 " 0.109 2.00e-02 2.50e+03 2.88e-01 1.87e+03 pdb=" C2A M1V K 801 " -0.095 2.00e-02 2.50e+03 pdb=" C3A M1V K 801 " 0.105 2.00e-02 2.50e+03 pdb=" C4A M1V K 801 " -0.057 2.00e-02 2.50e+03 pdb=" CAA M1V K 801 " 0.464 2.00e-02 2.50e+03 pdb=" CHA M1V K 801 " -0.449 2.00e-02 2.50e+03 pdb=" CMA M1V K 801 " -0.463 2.00e-02 2.50e+03 pdb=" NA M1V K 801 " 0.249 2.00e-02 2.50e+03 pdb=" OA M1V K 801 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C M1V C 201 " -0.007 2.00e-02 2.50e+03 2.39e-01 1.29e+03 pdb=" C2C M1V C 201 " 0.108 2.00e-02 2.50e+03 pdb=" C3C M1V C 201 " -0.012 2.00e-02 2.50e+03 pdb=" C4C M1V C 201 " 0.101 2.00e-02 2.50e+03 pdb=" CAC M1V C 201 " 0.251 2.00e-02 2.50e+03 pdb=" CHB M1V C 201 " -0.453 2.00e-02 2.50e+03 pdb=" CHC M1V C 201 " -0.079 2.00e-02 2.50e+03 pdb=" CMC M1V C 201 " -0.281 2.00e-02 2.50e+03 pdb=" NC M1V C 201 " 0.373 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C M1V K 801 " -0.011 2.00e-02 2.50e+03 2.02e-01 9.22e+02 pdb=" C2C M1V K 801 " -0.057 2.00e-02 2.50e+03 pdb=" C3C M1V K 801 " 0.014 2.00e-02 2.50e+03 pdb=" C4C M1V K 801 " -0.077 2.00e-02 2.50e+03 pdb=" CAC M1V K 801 " -0.169 2.00e-02 2.50e+03 pdb=" CHB M1V K 801 " 0.367 2.00e-02 2.50e+03 pdb=" CHC M1V K 801 " 0.141 2.00e-02 2.50e+03 pdb=" CMC M1V K 801 " 0.174 2.00e-02 2.50e+03 pdb=" NC M1V K 801 " -0.382 2.00e-02 2.50e+03 ... (remaining 4809 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 625 2.66 - 3.22: 26387 3.22 - 3.78: 49438 3.78 - 4.34: 64000 4.34 - 4.90: 102354 Nonbonded interactions: 242804 Sorted by model distance: nonbonded pdb=" OG SER E 139 " pdb=" OD1 ASP E 142 " model vdw 2.105 2.440 nonbonded pdb=" OG SER M 2 " pdb=" OD2 ASP N 3 " model vdw 2.142 2.440 nonbonded pdb=" O ILE P 51 " pdb=" OG1 THR P 55 " model vdw 2.147 2.440 nonbonded pdb=" O SER K 268 " pdb=" OG SER K 272 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" O LYS B 17 " model vdw 2.185 2.440 ... (remaining 242799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'G' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = (chain 'B' and (resid 2 through 160 or resid 201)) selection = (chain 'D' and (resid 2 through 160 or resid 201)) selection = (chain 'F' and (resid 2 through 160 or resid 201)) selection = (chain 'H' and (resid 2 through 160 or resid 201)) selection = chain 'L' selection = (chain 'N' and (resid 2 through 160 or resid 201)) selection = (chain 'P' and (resid 2 through 160 or resid 201)) selection = (chain 'R' and (resid 2 through 160 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.650 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 72.050 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.280 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 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 : 0.010 0.389 27522 Z= 0.670 Angle : 1.170 24.543 37298 Z= 0.585 Chirality : 0.061 1.020 4096 Planarity : 0.013 0.288 4812 Dihedral : 19.110 110.088 10714 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.88 % Favored : 96.91 % Rotamer: Outliers : 4.23 % Allowed : 29.75 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.61 (0.13), residues: 3300 helix: 0.09 (0.09), residues: 2599 sheet: 1.58 (1.47), residues: 17 loop : -2.03 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 84 HIS 0.015 0.002 HIS N 155 PHE 0.042 0.003 PHE P 88 TYR 0.059 0.004 TYR K 626 ARG 0.045 0.001 ARG J 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 558 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.5069 (t80) cc_final: 0.4607 (m-80) REVERT: A 110 LYS cc_start: 0.6989 (mmmm) cc_final: 0.6701 (mmmt) REVERT: B 8 LEU cc_start: 0.6634 (mt) cc_final: 0.6368 (mp) REVERT: B 17 LYS cc_start: 0.5863 (pttp) cc_final: 0.5606 (pttp) REVERT: B 119 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6246 (mp) REVERT: C 82 MET cc_start: 0.4292 (mmt) cc_final: 0.3140 (mmt) REVERT: E 38 ARG cc_start: 0.5892 (ttp-170) cc_final: 0.5602 (ttp80) REVERT: E 111 GLU cc_start: 0.6635 (pm20) cc_final: 0.6164 (tm-30) REVERT: E 152 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5552 (mm) REVERT: I 89 ILE cc_start: 0.7240 (mt) cc_final: 0.6914 (tt) REVERT: J 3 ASP cc_start: 0.3055 (OUTLIER) cc_final: 0.2851 (p0) REVERT: J 39 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6949 (mtmm) REVERT: J 153 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5622 (tp) REVERT: K 547 LEU cc_start: 0.7788 (mt) cc_final: 0.7462 (mt) REVERT: K 694 MET cc_start: 0.5005 (OUTLIER) cc_final: 0.4086 (tmm) REVERT: N 17 LYS cc_start: 0.6323 (ptpp) cc_final: 0.6005 (ptmm) REVERT: O 133 GLU cc_start: 0.3605 (OUTLIER) cc_final: 0.3273 (mp0) REVERT: P 85 MET cc_start: 0.6612 (mmp) cc_final: 0.6168 (mtt) REVERT: Q 35 GLN cc_start: 0.6509 (tt0) cc_final: 0.5912 (tp-100) REVERT: Q 98 GLU cc_start: 0.5366 (pp20) cc_final: 0.5142 (pp20) REVERT: Q 103 ASP cc_start: 0.6604 (m-30) cc_final: 0.6380 (m-30) outliers start: 118 outliers final: 65 residues processed: 644 average time/residue: 1.4375 time to fit residues: 1063.5029 Evaluate side-chains 588 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 517 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 258 LYS Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 113 LYS Chi-restraints excluded: chain O residue 55 SER Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 123 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 298 optimal weight: 0.0040 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 53 ASN A 79 GLN A 122 ASN B 47 ASN B 117 ASN C 79 GLN E 35 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN F 117 ASN G 27 GLN G 79 GLN G 122 ASN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 68 ASN I 71 ASN K 29 HIS K 37 HIS ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 451 GLN K 469 GLN K 476 HIS K 484 GLN K 564 HIS L 2 GLN L 10 ASN L 117 ASN M 52 GLN M 53 ASN M 79 GLN M 122 ASN O 68 ASN O 115 ASN P 110 ASN Q 53 ASN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 GLN R 117 ASN R 138 ASN S 63 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27522 Z= 0.205 Angle : 0.684 10.028 37298 Z= 0.329 Chirality : 0.040 0.208 4096 Planarity : 0.005 0.067 4812 Dihedral : 10.194 108.066 4652 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.76 % Favored : 97.03 % Rotamer: Outliers : 6.92 % Allowed : 25.52 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.39 (0.14), residues: 3300 helix: 0.88 (0.10), residues: 2596 sheet: 2.22 (1.36), residues: 15 loop : -2.03 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 59 HIS 0.014 0.001 HIS K 29 PHE 0.026 0.002 PHE P 88 TYR 0.027 0.002 TYR L 151 ARG 0.008 0.001 ARG K 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 559 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 SER cc_start: 0.5516 (p) cc_final: 0.5275 (t) REVERT: A 110 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6802 (mmmt) REVERT: A 152 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6237 (mm) REVERT: B 8 LEU cc_start: 0.6619 (mt) cc_final: 0.6415 (mp) REVERT: B 17 LYS cc_start: 0.5778 (pttp) cc_final: 0.5546 (pttp) REVERT: B 85 MET cc_start: 0.3933 (mmm) cc_final: 0.3460 (mmt) REVERT: C 53 ARG cc_start: 0.5877 (OUTLIER) cc_final: 0.5304 (mtm-85) REVERT: C 82 MET cc_start: 0.4271 (OUTLIER) cc_final: 0.2838 (mmt) REVERT: C 120 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6755 (mt) REVERT: C 146 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6039 (pp) REVERT: C 147 ILE cc_start: 0.7357 (mm) cc_final: 0.7150 (mm) REVERT: D 76 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7473 (ptt90) REVERT: D 87 PHE cc_start: 0.7565 (m-80) cc_final: 0.7343 (m-80) REVERT: F 42 MET cc_start: 0.5345 (mtp) cc_final: 0.4806 (mmm) REVERT: G 98 GLU cc_start: 0.6072 (pm20) cc_final: 0.5448 (pm20) REVERT: H 140 MET cc_start: 0.4891 (pmm) cc_final: 0.4453 (pp-130) REVERT: H 147 LYS cc_start: 0.5198 (ptmm) cc_final: 0.4459 (mmmm) REVERT: I 107 ARG cc_start: 0.6379 (tpt90) cc_final: 0.6148 (tpt170) REVERT: J 29 SER cc_start: 0.7808 (t) cc_final: 0.7565 (p) REVERT: J 39 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6771 (mtmm) REVERT: K 543 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5372 (mm-30) REVERT: K 626 TYR cc_start: 0.5781 (m-80) cc_final: 0.5259 (m-80) REVERT: K 694 MET cc_start: 0.4983 (OUTLIER) cc_final: 0.4330 (mmm) REVERT: L 44 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7278 (tp) REVERT: L 107 ARG cc_start: 0.5562 (tpp-160) cc_final: 0.5110 (mmt90) REVERT: M 98 GLU cc_start: 0.5877 (OUTLIER) cc_final: 0.5347 (pm20) REVERT: M 110 LYS cc_start: 0.6291 (mmmt) cc_final: 0.5984 (mmmt) REVERT: N 17 LYS cc_start: 0.6297 (ptpp) cc_final: 0.6004 (ptmm) REVERT: N 134 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6319 (tttt) REVERT: O 29 PHE cc_start: 0.6201 (t80) cc_final: 0.5921 (t80) REVERT: O 57 LYS cc_start: 0.4797 (ptmt) cc_final: 0.4489 (ptpt) REVERT: O 133 GLU cc_start: 0.3973 (OUTLIER) cc_final: 0.3753 (mp0) REVERT: P 85 MET cc_start: 0.6425 (mmp) cc_final: 0.6013 (mtt) REVERT: P 135 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: Q 35 GLN cc_start: 0.6297 (tt0) cc_final: 0.5778 (tp-100) REVERT: Q 128 ARG cc_start: 0.5522 (mtt180) cc_final: 0.5243 (mtt180) REVERT: R 97 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7541 (tp) outliers start: 193 outliers final: 66 residues processed: 680 average time/residue: 1.4238 time to fit residues: 1114.2209 Evaluate side-chains 591 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 510 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 281 MET Chi-restraints excluded: chain K residue 543 GLU Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 135 GLU Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 296 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 240 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 10 ASN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 29 HIS K 212 GLN K 215 GLN K 396 GLN K 463 ASN K 469 GLN K 476 HIS M 52 GLN N 10 ASN N 110 ASN O 53 ASN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN S 63 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27522 Z= 0.272 Angle : 0.736 11.139 37298 Z= 0.355 Chirality : 0.042 0.243 4096 Planarity : 0.005 0.065 4812 Dihedral : 9.799 105.376 4584 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.15 % Favored : 96.64 % Rotamer: Outliers : 7.99 % Allowed : 25.52 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.37 (0.14), residues: 3300 helix: 0.87 (0.10), residues: 2585 sheet: 0.06 (1.27), residues: 19 loop : -1.96 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 59 HIS 0.011 0.001 HIS K 29 PHE 0.019 0.002 PHE K 554 TYR 0.034 0.002 TYR H 152 ARG 0.011 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 554 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7300 (mmmm) cc_final: 0.6949 (mmmt) REVERT: B 8 LEU cc_start: 0.6719 (mt) cc_final: 0.6472 (mp) REVERT: B 17 LYS cc_start: 0.5817 (pttp) cc_final: 0.5586 (pttp) REVERT: B 85 MET cc_start: 0.4121 (mmm) cc_final: 0.3642 (mmt) REVERT: C 25 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5755 (tpt) REVERT: C 53 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5441 (mtm-85) REVERT: C 82 MET cc_start: 0.4309 (OUTLIER) cc_final: 0.2782 (mmp) REVERT: C 120 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6849 (mt) REVERT: C 130 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7148 (mp) REVERT: C 146 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6159 (pp) REVERT: D 1 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4678 (ptp) REVERT: D 76 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7501 (ptt90) REVERT: E 38 ARG cc_start: 0.5681 (ttp-170) cc_final: 0.5434 (ttp80) REVERT: E 93 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6605 (mt) REVERT: F 100 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.6319 (t0) REVERT: F 133 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6295 (ttm) REVERT: G 16 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6429 (ptm160) REVERT: G 47 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5853 (tt0) REVERT: G 73 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5644 (ppp80) REVERT: G 98 GLU cc_start: 0.6139 (pm20) cc_final: 0.5539 (pm20) REVERT: G 123 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7408 (mm) REVERT: G 127 MET cc_start: 0.6604 (tpp) cc_final: 0.6317 (mpm) REVERT: H 100 ASP cc_start: 0.6085 (t70) cc_final: 0.5625 (t0) REVERT: H 147 LYS cc_start: 0.5256 (ptmm) cc_final: 0.4484 (mmmm) REVERT: J 21 ARG cc_start: 0.1941 (OUTLIER) cc_final: 0.0916 (tpt170) REVERT: J 29 SER cc_start: 0.7900 (t) cc_final: 0.7690 (p) REVERT: J 39 LYS cc_start: 0.7077 (mtmt) cc_final: 0.6852 (mtmm) REVERT: K 163 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.5312 (tptp) REVERT: K 166 MET cc_start: 0.5812 (mmp) cc_final: 0.5389 (mmm) REVERT: K 342 ARG cc_start: 0.4947 (mtm110) cc_final: 0.4401 (mtp85) REVERT: K 360 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6672 (tmt170) REVERT: K 543 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5398 (mm-30) REVERT: K 626 TYR cc_start: 0.5838 (m-80) cc_final: 0.5336 (m-80) REVERT: K 694 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4163 (mmm) REVERT: K 695 ARG cc_start: 0.4396 (OUTLIER) cc_final: 0.3588 (mtp180) REVERT: L 19 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6137 (mp) REVERT: L 96 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6533 (ttm) REVERT: M 98 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5395 (pm20) REVERT: M 111 GLU cc_start: 0.5761 (pm20) cc_final: 0.5468 (pm20) REVERT: N 1 MET cc_start: 0.4738 (tmt) cc_final: 0.3891 (ptm) REVERT: N 8 LEU cc_start: 0.6551 (mt) cc_final: 0.6263 (mp) REVERT: N 76 ARG cc_start: 0.5965 (ptm-80) cc_final: 0.5445 (ttp80) REVERT: N 134 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6518 (tttt) REVERT: O 29 PHE cc_start: 0.6185 (t80) cc_final: 0.5894 (t80) REVERT: O 152 LEU cc_start: 0.5843 (OUTLIER) cc_final: 0.5623 (mp) REVERT: P 11 THR cc_start: 0.6694 (p) cc_final: 0.6472 (t) REVERT: P 85 MET cc_start: 0.6534 (mmp) cc_final: 0.6068 (mtp) REVERT: Q 98 GLU cc_start: 0.5276 (pp20) cc_final: 0.4921 (pp20) REVERT: Q 125 GLU cc_start: 0.5493 (OUTLIER) cc_final: 0.4893 (tp30) REVERT: R 76 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5384 (ptt90) REVERT: R 97 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7579 (tp) outliers start: 223 outliers final: 96 residues processed: 700 average time/residue: 1.5228 time to fit residues: 1225.4931 Evaluate side-chains 648 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 523 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain K residue 163 LYS Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 360 ARG Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 543 GLU Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 694 MET Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 CYS Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 284 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 10 ASN ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN F 117 ASN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 29 HIS ** K 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 476 HIS M 52 GLN N 2 GLN N 10 ASN O 35 GLN O 53 ASN P 138 ASN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN S 63 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27522 Z= 0.266 Angle : 0.722 10.391 37298 Z= 0.350 Chirality : 0.042 0.252 4096 Planarity : 0.005 0.064 4812 Dihedral : 9.692 101.538 4578 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 7.42 % Allowed : 27.24 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.38 (0.14), residues: 3300 helix: 0.86 (0.10), residues: 2588 sheet: 0.13 (1.32), residues: 19 loop : -1.93 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 59 HIS 0.008 0.001 HIS K 29 PHE 0.017 0.002 PHE K 554 TYR 0.031 0.002 TYR H 152 ARG 0.010 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 556 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 GLN cc_start: 0.5665 (mm-40) cc_final: 0.5358 (mm-40) REVERT: B 17 LYS cc_start: 0.5855 (pttp) cc_final: 0.5610 (pttp) REVERT: B 77 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7477 (mtp180) REVERT: B 85 MET cc_start: 0.4321 (mmm) cc_final: 0.3880 (mmt) REVERT: C 39 LEU cc_start: 0.7201 (mm) cc_final: 0.6981 (mt) REVERT: C 53 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5482 (mtm-85) REVERT: C 120 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6869 (mt) REVERT: C 137 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6432 (tt) REVERT: C 146 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6108 (pp) REVERT: D 10 ASN cc_start: 0.6128 (m-40) cc_final: 0.5464 (m110) REVERT: D 76 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7425 (ptt90) REVERT: E 60 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5493 (mp0) REVERT: E 93 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6600 (mt) REVERT: E 135 MET cc_start: 0.5934 (mmm) cc_final: 0.5694 (mmm) REVERT: E 142 ASP cc_start: 0.5997 (m-30) cc_final: 0.5724 (m-30) REVERT: F 136 VAL cc_start: 0.6292 (t) cc_final: 0.5958 (p) REVERT: G 16 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6402 (ptm160) REVERT: G 47 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5733 (tt0) REVERT: G 73 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5646 (ppp80) REVERT: G 98 GLU cc_start: 0.6212 (pm20) cc_final: 0.5605 (pm20) REVERT: G 127 MET cc_start: 0.6594 (tpp) cc_final: 0.6244 (mpt) REVERT: G 135 MET cc_start: 0.5859 (mmp) cc_final: 0.5455 (mmp) REVERT: H 147 LYS cc_start: 0.5229 (ptmm) cc_final: 0.4523 (mmmm) REVERT: I 53 LYS cc_start: 0.7368 (mtpt) cc_final: 0.7146 (mtpm) REVERT: J 21 ARG cc_start: 0.1941 (OUTLIER) cc_final: 0.0936 (tpt170) REVERT: J 29 SER cc_start: 0.7891 (t) cc_final: 0.7666 (m) REVERT: J 39 LYS cc_start: 0.7029 (mtmt) cc_final: 0.6644 (mtmm) REVERT: J 139 LYS cc_start: 0.7211 (tptp) cc_final: 0.6944 (tptp) REVERT: K 25 ILE cc_start: 0.6561 (mt) cc_final: 0.6279 (tp) REVERT: K 360 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6545 (tmt170) REVERT: K 626 TYR cc_start: 0.5769 (m-80) cc_final: 0.5194 (m-80) REVERT: K 692 TYR cc_start: 0.6171 (t80) cc_final: 0.5898 (t80) REVERT: K 695 ARG cc_start: 0.4342 (OUTLIER) cc_final: 0.3241 (mtp180) REVERT: L 19 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.6006 (mp) REVERT: L 96 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6537 (ttm) REVERT: M 98 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5402 (pm20) REVERT: M 110 LYS cc_start: 0.6531 (mmmt) cc_final: 0.6239 (mmmt) REVERT: M 111 GLU cc_start: 0.5694 (pm20) cc_final: 0.5446 (pm20) REVERT: N 1 MET cc_start: 0.4783 (tmt) cc_final: 0.4433 (tmt) REVERT: N 8 LEU cc_start: 0.6572 (mt) cc_final: 0.6318 (mp) REVERT: N 17 LYS cc_start: 0.6507 (ptpp) cc_final: 0.6132 (ptmm) REVERT: N 134 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6465 (tttt) REVERT: O 29 PHE cc_start: 0.6265 (t80) cc_final: 0.5934 (t80) REVERT: O 152 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5634 (mp) REVERT: P 53 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7334 (m) REVERT: P 85 MET cc_start: 0.6551 (mmp) cc_final: 0.6144 (mtt) REVERT: Q 98 GLU cc_start: 0.5139 (pp20) cc_final: 0.4826 (pp20) REVERT: Q 125 GLU cc_start: 0.5521 (OUTLIER) cc_final: 0.4744 (tp30) REVERT: R 76 ARG cc_start: 0.6011 (OUTLIER) cc_final: 0.5357 (ptt90) REVERT: R 97 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7581 (tp) REVERT: S 46 MET cc_start: 0.5762 (mtm) cc_final: 0.5483 (ptt) outliers start: 207 outliers final: 102 residues processed: 696 average time/residue: 1.4835 time to fit residues: 1186.5794 Evaluate side-chains 644 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 520 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 360 ARG Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 CYS Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 154 ILE Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 236 optimal weight: 0.0040 chunk 131 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 285 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS C 68 ASN ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 115 ASN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 26 ASN K 29 HIS K 316 GLN ** K 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 ASN K 476 HIS M 52 GLN O 35 GLN O 53 ASN P 28 GLN P 138 ASN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27522 Z= 0.256 Angle : 0.719 11.151 37298 Z= 0.349 Chirality : 0.042 0.244 4096 Planarity : 0.005 0.063 4812 Dihedral : 9.495 98.513 4565 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % Rotamer: Outliers : 8.03 % Allowed : 27.31 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.45 (0.14), residues: 3300 helix: 0.91 (0.10), residues: 2587 sheet: 0.17 (1.35), residues: 19 loop : -1.90 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 59 HIS 0.008 0.001 HIS K 29 PHE 0.016 0.002 PHE K 554 TYR 0.031 0.002 TYR B 152 ARG 0.011 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 549 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.5928 (pttp) cc_final: 0.5690 (pttp) REVERT: B 85 MET cc_start: 0.4192 (mmm) cc_final: 0.3812 (mmt) REVERT: C 53 ARG cc_start: 0.6077 (OUTLIER) cc_final: 0.5873 (mtm-85) REVERT: C 102 ARG cc_start: 0.6026 (mtm110) cc_final: 0.5467 (mtm180) REVERT: C 120 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6833 (mt) REVERT: C 146 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6098 (pp) REVERT: D 10 ASN cc_start: 0.6127 (m-40) cc_final: 0.5442 (m110) REVERT: D 32 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5161 (mpt-90) REVERT: D 76 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7413 (ptt90) REVERT: E 60 GLU cc_start: 0.5634 (mp0) cc_final: 0.5419 (mp0) REVERT: E 93 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6568 (mt) REVERT: F 42 MET cc_start: 0.5180 (mtp) cc_final: 0.4954 (tpp) REVERT: F 54 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.6251 (mtpp) REVERT: F 58 LYS cc_start: 0.6659 (ptmt) cc_final: 0.6355 (ptpt) REVERT: G 16 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6396 (ptm160) REVERT: G 24 ARG cc_start: 0.5843 (ttp-170) cc_final: 0.5515 (ttm170) REVERT: G 47 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5748 (tt0) REVERT: G 79 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5776 (tp40) REVERT: G 98 GLU cc_start: 0.6174 (pm20) cc_final: 0.5604 (pm20) REVERT: G 123 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7418 (mm) REVERT: G 127 MET cc_start: 0.6616 (tpp) cc_final: 0.5596 (mpm) REVERT: G 135 MET cc_start: 0.5978 (mmp) cc_final: 0.5440 (mmp) REVERT: G 150 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.4988 (t80) REVERT: H 100 ASP cc_start: 0.6051 (t70) cc_final: 0.5569 (t0) REVERT: H 147 LYS cc_start: 0.5236 (ptmm) cc_final: 0.4531 (mmmm) REVERT: I 89 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7016 (tt) REVERT: J 21 ARG cc_start: 0.2108 (OUTLIER) cc_final: 0.1043 (tpt170) REVERT: J 29 SER cc_start: 0.7846 (t) cc_final: 0.7614 (m) REVERT: J 39 LYS cc_start: 0.7031 (mtmt) cc_final: 0.6648 (mtmm) REVERT: J 58 LYS cc_start: 0.6034 (ttmt) cc_final: 0.5620 (mtmt) REVERT: K 166 MET cc_start: 0.5566 (mmp) cc_final: 0.5220 (mmm) REVERT: K 360 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6541 (tmt170) REVERT: K 626 TYR cc_start: 0.5750 (m-80) cc_final: 0.5112 (m-80) REVERT: K 692 TYR cc_start: 0.6086 (t80) cc_final: 0.5821 (t80) REVERT: K 693 MET cc_start: 0.6493 (mmm) cc_final: 0.6208 (mmm) REVERT: K 695 ARG cc_start: 0.4291 (OUTLIER) cc_final: 0.2914 (mtp180) REVERT: L 19 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6127 (mp) REVERT: L 76 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6340 (ptm-80) REVERT: L 96 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6549 (ttm) REVERT: M 98 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5362 (pm20) REVERT: M 157 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.4136 (mm) REVERT: N 1 MET cc_start: 0.4729 (tmt) cc_final: 0.3857 (ptm) REVERT: N 8 LEU cc_start: 0.6566 (mt) cc_final: 0.6343 (mp) REVERT: N 17 LYS cc_start: 0.6530 (ptpp) cc_final: 0.6151 (ptmm) REVERT: N 134 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6430 (tttt) REVERT: O 29 PHE cc_start: 0.6268 (t80) cc_final: 0.5955 (t80) REVERT: O 152 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5675 (tp) REVERT: P 53 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7300 (m) REVERT: P 85 MET cc_start: 0.6543 (mmp) cc_final: 0.6178 (mtt) REVERT: Q 98 GLU cc_start: 0.5083 (pp20) cc_final: 0.4722 (pp20) REVERT: Q 125 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5126 (tp30) REVERT: R 76 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5295 (ptt90) REVERT: R 96 MET cc_start: 0.7342 (tmm) cc_final: 0.7016 (ttp) REVERT: R 97 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7585 (tp) REVERT: R 110 ASN cc_start: 0.6099 (OUTLIER) cc_final: 0.5819 (p0) REVERT: S 46 MET cc_start: 0.5667 (mtm) cc_final: 0.5374 (ptt) REVERT: S 54 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6182 (tp30) outliers start: 224 outliers final: 111 residues processed: 704 average time/residue: 1.4808 time to fit residues: 1197.1597 Evaluate side-chains 657 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 518 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 32 ARG Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 154 ASP Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 272 SER Chi-restraints excluded: chain K residue 360 ARG Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 646 ASP Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 118 SER Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 157 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 75 CYS Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain R residue 8 LEU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 9.9990 chunk 286 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 318 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 GLN B 10 ASN B 155 HIS C 68 ASN D 2 GLN D 10 ASN D 15 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 29 HIS K 463 ASN K 476 HIS M 52 GLN O 35 GLN P 28 GLN P 138 ASN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27522 Z= 0.195 Angle : 0.665 11.786 37298 Z= 0.322 Chirality : 0.040 0.226 4096 Planarity : 0.005 0.061 4812 Dihedral : 9.278 92.697 4561 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.82 % Favored : 97.00 % Rotamer: Outliers : 6.59 % Allowed : 28.92 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.87 (0.15), residues: 3300 helix: 1.22 (0.10), residues: 2585 sheet: 0.23 (1.34), residues: 19 loop : -1.79 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 84 HIS 0.009 0.001 HIS K 29 PHE 0.016 0.001 PHE A 150 TYR 0.027 0.002 TYR B 152 ARG 0.010 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 570 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.5783 (pttp) cc_final: 0.5565 (pttp) REVERT: B 27 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.4259 (tt) REVERT: B 85 MET cc_start: 0.4184 (mmm) cc_final: 0.3826 (mmt) REVERT: C 9 SER cc_start: 0.7671 (m) cc_final: 0.7450 (t) REVERT: C 53 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5827 (mtm-85) REVERT: C 98 ASP cc_start: 0.6656 (p0) cc_final: 0.6362 (p0) REVERT: C 102 ARG cc_start: 0.5929 (mtm110) cc_final: 0.5240 (mtm180) REVERT: C 146 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6024 (pp) REVERT: D 1 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.4178 (ptp) REVERT: D 58 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6815 (ptmt) REVERT: D 103 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6698 (tp) REVERT: E 60 GLU cc_start: 0.5617 (mp0) cc_final: 0.5374 (mp0) REVERT: E 93 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6498 (mt) REVERT: F 28 GLN cc_start: 0.5738 (mt0) cc_final: 0.5358 (mm110) REVERT: F 42 MET cc_start: 0.5180 (mtp) cc_final: 0.4755 (tpp) REVERT: F 58 LYS cc_start: 0.6683 (ptmt) cc_final: 0.6357 (ptpt) REVERT: G 16 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6606 (ptm160) REVERT: G 24 ARG cc_start: 0.5777 (ttp-170) cc_final: 0.5491 (ttm170) REVERT: G 73 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5588 (ppp80) REVERT: G 98 GLU cc_start: 0.6163 (pm20) cc_final: 0.5594 (pm20) REVERT: G 123 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7455 (mm) REVERT: G 127 MET cc_start: 0.6568 (tpp) cc_final: 0.5496 (mpm) REVERT: G 135 MET cc_start: 0.5840 (mmp) cc_final: 0.5377 (mmp) REVERT: G 150 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.4893 (t80) REVERT: H 100 ASP cc_start: 0.5948 (t70) cc_final: 0.5428 (t0) REVERT: H 147 LYS cc_start: 0.5298 (ptmm) cc_final: 0.4559 (mmmm) REVERT: I 158 MET cc_start: 0.5727 (tpp) cc_final: 0.4932 (ptm) REVERT: J 21 ARG cc_start: 0.1864 (OUTLIER) cc_final: 0.0729 (tpt170) REVERT: J 29 SER cc_start: 0.7807 (t) cc_final: 0.7606 (p) REVERT: J 39 LYS cc_start: 0.7123 (mtmt) cc_final: 0.6720 (mtmm) REVERT: J 58 LYS cc_start: 0.6003 (ttmt) cc_final: 0.5569 (mtmt) REVERT: K 272 SER cc_start: 0.6588 (p) cc_final: 0.6280 (p) REVERT: K 295 ARG cc_start: 0.6485 (mtm-85) cc_final: 0.6129 (mtm110) REVERT: K 691 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5690 (pp20) REVERT: K 692 TYR cc_start: 0.5957 (t80) cc_final: 0.5634 (t80) REVERT: K 695 ARG cc_start: 0.3949 (OUTLIER) cc_final: 0.2221 (mtp180) REVERT: L 76 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6330 (ptm-80) REVERT: L 96 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6544 (ttm) REVERT: M 73 ARG cc_start: 0.6565 (tmm160) cc_final: 0.6272 (tmm160) REVERT: N 1 MET cc_start: 0.4730 (tmt) cc_final: 0.4000 (ptm) REVERT: N 8 LEU cc_start: 0.6483 (mt) cc_final: 0.6275 (mp) REVERT: N 17 LYS cc_start: 0.6406 (ptpp) cc_final: 0.6053 (ptmm) REVERT: N 76 ARG cc_start: 0.5938 (ttp80) cc_final: 0.5640 (tmt-80) REVERT: N 106 GLU cc_start: 0.6024 (mm-30) cc_final: 0.5693 (mp0) REVERT: N 134 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6432 (tttt) REVERT: O 24 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.4755 (tpm170) REVERT: O 29 PHE cc_start: 0.6353 (t80) cc_final: 0.6015 (t80) REVERT: O 133 GLU cc_start: 0.3683 (OUTLIER) cc_final: 0.3347 (mp0) REVERT: P 28 GLN cc_start: 0.5607 (OUTLIER) cc_final: 0.4834 (mp-120) REVERT: P 53 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7286 (m) REVERT: P 85 MET cc_start: 0.6616 (mmp) cc_final: 0.6118 (mtt) REVERT: Q 98 GLU cc_start: 0.5090 (pp20) cc_final: 0.4686 (pp20) REVERT: Q 125 GLU cc_start: 0.5545 (OUTLIER) cc_final: 0.5011 (tp30) REVERT: Q 152 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5774 (tp) REVERT: R 76 ARG cc_start: 0.5914 (OUTLIER) cc_final: 0.5274 (ptt90) REVERT: R 96 MET cc_start: 0.7252 (tmm) cc_final: 0.6915 (ttp) REVERT: R 110 ASN cc_start: 0.6101 (OUTLIER) cc_final: 0.5631 (p0) REVERT: S 45 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6528 (mptm) REVERT: S 54 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6055 (tp30) outliers start: 184 outliers final: 77 residues processed: 694 average time/residue: 1.5170 time to fit residues: 1211.4324 Evaluate side-chains 634 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 531 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 382 ASP Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 646 ASP Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 75 CYS Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 267 optimal weight: 0.2980 chunk 177 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 146 optimal weight: 0.0770 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 2 GLN B 155 HIS C 68 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN G 35 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN I 68 ASN I 71 ASN J 101 ASN K 26 ASN K 29 HIS K 463 ASN K 476 HIS M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27522 Z= 0.221 Angle : 0.693 11.167 37298 Z= 0.336 Chirality : 0.041 0.231 4096 Planarity : 0.005 0.061 4812 Dihedral : 9.164 90.702 4557 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 6.42 % Allowed : 29.14 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.82 (0.15), residues: 3300 helix: 1.18 (0.10), residues: 2591 sheet: 0.46 (1.36), residues: 19 loop : -1.80 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 84 HIS 0.008 0.001 HIS K 29 PHE 0.013 0.002 PHE K 554 TYR 0.032 0.002 TYR B 152 ARG 0.010 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 542 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6751 (tp) cc_final: 0.6432 (pp) REVERT: A 110 LYS cc_start: 0.7215 (mmmt) cc_final: 0.6803 (mmmt) REVERT: A 133 GLU cc_start: 0.3736 (OUTLIER) cc_final: 0.3497 (mp0) REVERT: B 17 LYS cc_start: 0.5809 (pttp) cc_final: 0.5542 (pttp) REVERT: B 85 MET cc_start: 0.4267 (mmm) cc_final: 0.3906 (mmt) REVERT: B 151 TYR cc_start: 0.5068 (t80) cc_final: 0.4465 (t80) REVERT: C 9 SER cc_start: 0.7634 (m) cc_final: 0.7420 (t) REVERT: C 53 ARG cc_start: 0.6027 (OUTLIER) cc_final: 0.5818 (mtm-85) REVERT: C 60 GLN cc_start: 0.5368 (OUTLIER) cc_final: 0.5073 (mp10) REVERT: C 98 ASP cc_start: 0.6682 (p0) cc_final: 0.6412 (p0) REVERT: C 102 ARG cc_start: 0.5948 (mtm110) cc_final: 0.5367 (mtm180) REVERT: C 146 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6137 (pp) REVERT: D 1 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.4413 (ptp) REVERT: D 58 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6845 (ptmt) REVERT: D 103 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6720 (tp) REVERT: E 38 ARG cc_start: 0.5564 (ttp80) cc_final: 0.4975 (ttp-170) REVERT: E 60 GLU cc_start: 0.5634 (mp0) cc_final: 0.5408 (mp0) REVERT: E 93 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6498 (mt) REVERT: E 121 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.5258 (ppp80) REVERT: F 28 GLN cc_start: 0.5633 (mt0) cc_final: 0.5385 (mm-40) REVERT: F 42 MET cc_start: 0.5184 (mtp) cc_final: 0.4766 (tpp) REVERT: F 58 LYS cc_start: 0.6635 (ptmt) cc_final: 0.6324 (ptpt) REVERT: G 16 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6629 (ptm160) REVERT: G 24 ARG cc_start: 0.5742 (ttp-170) cc_final: 0.5528 (ttm170) REVERT: G 73 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5668 (ppp80) REVERT: G 98 GLU cc_start: 0.6148 (pm20) cc_final: 0.5593 (pm20) REVERT: G 123 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7435 (mm) REVERT: G 127 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.5496 (mpm) REVERT: G 135 MET cc_start: 0.5910 (mmp) cc_final: 0.5405 (mmp) REVERT: G 150 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.4897 (t80) REVERT: H 100 ASP cc_start: 0.6054 (t70) cc_final: 0.5543 (t0) REVERT: H 147 LYS cc_start: 0.5333 (OUTLIER) cc_final: 0.4589 (mmmm) REVERT: I 89 ILE cc_start: 0.7335 (mt) cc_final: 0.6980 (tt) REVERT: I 158 MET cc_start: 0.5733 (tpp) cc_final: 0.4914 (ptm) REVERT: J 21 ARG cc_start: 0.1906 (OUTLIER) cc_final: 0.0751 (tpt170) REVERT: J 24 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5821 (mt) REVERT: J 29 SER cc_start: 0.7806 (t) cc_final: 0.7597 (p) REVERT: J 39 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6779 (mtmm) REVERT: K 272 SER cc_start: 0.6614 (p) cc_final: 0.6294 (p) REVERT: K 493 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6910 (mtm180) REVERT: K 691 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5766 (pp20) REVERT: K 692 TYR cc_start: 0.6001 (t80) cc_final: 0.5744 (t80) REVERT: L 76 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6356 (ptm-80) REVERT: L 96 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6520 (ttm) REVERT: M 57 LYS cc_start: 0.5817 (mmtp) cc_final: 0.5611 (mppt) REVERT: M 110 LYS cc_start: 0.6385 (mmmt) cc_final: 0.6161 (tppp) REVERT: N 1 MET cc_start: 0.4752 (tmt) cc_final: 0.4002 (ptm) REVERT: N 8 LEU cc_start: 0.6478 (mt) cc_final: 0.6274 (mp) REVERT: N 17 LYS cc_start: 0.6408 (ptpp) cc_final: 0.6060 (ptmm) REVERT: N 76 ARG cc_start: 0.5963 (ttp80) cc_final: 0.5729 (ttp80) REVERT: N 105 ASP cc_start: 0.6582 (m-30) cc_final: 0.6334 (m-30) REVERT: N 106 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5822 (mp0) REVERT: N 134 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6462 (tttt) REVERT: O 24 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.4754 (tpm170) REVERT: O 29 PHE cc_start: 0.6390 (t80) cc_final: 0.6081 (t80) REVERT: O 152 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5419 (mt) REVERT: P 53 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7290 (m) REVERT: P 85 MET cc_start: 0.6619 (mmp) cc_final: 0.6112 (mtt) REVERT: Q 98 GLU cc_start: 0.5059 (pp20) cc_final: 0.4672 (pp20) REVERT: Q 125 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.4950 (tp30) REVERT: Q 152 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5754 (tp) REVERT: R 76 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5186 (ptt90) REVERT: R 96 MET cc_start: 0.7267 (tmm) cc_final: 0.6906 (ttp) REVERT: R 110 ASN cc_start: 0.6108 (OUTLIER) cc_final: 0.5620 (p0) REVERT: S 45 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6529 (mptm) REVERT: S 54 GLU cc_start: 0.6471 (mm-30) cc_final: 0.6018 (tp30) outliers start: 179 outliers final: 94 residues processed: 660 average time/residue: 1.5164 time to fit residues: 1146.7137 Evaluate side-chains 649 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 526 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 263 LEU Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 628 ASP Chi-restraints excluded: chain K residue 646 ASP Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 20 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 75 CYS Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 152 LEU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 201 optimal weight: 0.0370 chunk 216 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 29 optimal weight: 0.0870 chunk 249 optimal weight: 0.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN H 117 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 26 ASN K 29 HIS K 383 GLN ** K 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN P 138 ASN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27522 Z= 0.266 Angle : 0.736 14.145 37298 Z= 0.358 Chirality : 0.043 0.321 4096 Planarity : 0.005 0.061 4812 Dihedral : 9.181 90.450 4557 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.52 % Favored : 96.27 % Rotamer: Outliers : 6.81 % Allowed : 28.64 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.63 (0.15), residues: 3300 helix: 1.05 (0.10), residues: 2589 sheet: 0.49 (1.38), residues: 19 loop : -1.89 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.006 0.001 HIS K 457 PHE 0.016 0.002 PHE S 37 TYR 0.035 0.002 TYR L 152 ARG 0.011 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 549 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.6772 (tp) cc_final: 0.6436 (pp) REVERT: B 17 LYS cc_start: 0.5932 (pttp) cc_final: 0.5702 (pttp) REVERT: B 77 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7467 (mtp180) REVERT: B 151 TYR cc_start: 0.5138 (t80) cc_final: 0.4568 (t80) REVERT: C 53 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5942 (mtm-85) REVERT: C 60 GLN cc_start: 0.5407 (OUTLIER) cc_final: 0.5111 (mp10) REVERT: C 98 ASP cc_start: 0.6716 (p0) cc_final: 0.6428 (p0) REVERT: C 102 ARG cc_start: 0.5936 (mtm110) cc_final: 0.5336 (mtm180) REVERT: C 146 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.5935 (pp) REVERT: D 1 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5674 (pmt) REVERT: E 38 ARG cc_start: 0.5565 (ttp80) cc_final: 0.4993 (ttp-170) REVERT: E 60 GLU cc_start: 0.5760 (mp0) cc_final: 0.5537 (mp0) REVERT: E 93 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6578 (mt) REVERT: E 121 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.5166 (ppp80) REVERT: F 42 MET cc_start: 0.5259 (mtp) cc_final: 0.4882 (tpp) REVERT: F 54 LYS cc_start: 0.6390 (OUTLIER) cc_final: 0.6166 (mtpp) REVERT: F 58 LYS cc_start: 0.6679 (ptmt) cc_final: 0.6378 (ptpt) REVERT: F 136 VAL cc_start: 0.6333 (t) cc_final: 0.6009 (p) REVERT: G 16 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6649 (ptm160) REVERT: G 24 ARG cc_start: 0.5756 (ttp-170) cc_final: 0.5483 (ttm170) REVERT: G 73 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5686 (ppp80) REVERT: G 98 GLU cc_start: 0.6227 (pm20) cc_final: 0.5664 (pm20) REVERT: G 123 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7435 (mm) REVERT: G 127 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5528 (mpm) REVERT: G 135 MET cc_start: 0.6069 (mmp) cc_final: 0.5528 (mmp) REVERT: G 150 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.4950 (t80) REVERT: H 147 LYS cc_start: 0.5314 (OUTLIER) cc_final: 0.4593 (mmmm) REVERT: I 89 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7033 (tt) REVERT: I 158 MET cc_start: 0.5825 (tpp) cc_final: 0.4893 (ptt) REVERT: J 21 ARG cc_start: 0.2076 (OUTLIER) cc_final: 0.1004 (tpt170) REVERT: J 29 SER cc_start: 0.7842 (t) cc_final: 0.7621 (m) REVERT: J 39 LYS cc_start: 0.7064 (mtmt) cc_final: 0.6695 (mtmm) REVERT: J 58 LYS cc_start: 0.6026 (ttmt) cc_final: 0.5677 (mtmt) REVERT: J 78 ARG cc_start: 0.6893 (mmm-85) cc_final: 0.6489 (mtm-85) REVERT: K 272 SER cc_start: 0.6678 (p) cc_final: 0.6362 (p) REVERT: K 593 GLN cc_start: 0.6701 (mm110) cc_final: 0.6492 (mm-40) REVERT: K 626 TYR cc_start: 0.5752 (m-80) cc_final: 0.4863 (m-80) REVERT: K 691 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5865 (pp20) REVERT: K 692 TYR cc_start: 0.6052 (t80) cc_final: 0.5814 (t80) REVERT: L 76 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6366 (ptm-80) REVERT: L 96 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6507 (ttm) REVERT: M 73 ARG cc_start: 0.6548 (tmm160) cc_final: 0.6266 (tmm160) REVERT: M 98 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5421 (pm20) REVERT: M 110 LYS cc_start: 0.6386 (mmmt) cc_final: 0.6150 (tppp) REVERT: M 135 MET cc_start: 0.0879 (mmt) cc_final: 0.0611 (mmt) REVERT: N 1 MET cc_start: 0.4744 (tmt) cc_final: 0.4544 (tmt) REVERT: N 15 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5835 (mm-40) REVERT: N 17 LYS cc_start: 0.6422 (ptpp) cc_final: 0.6059 (ptmm) REVERT: N 76 ARG cc_start: 0.5982 (ttp80) cc_final: 0.5710 (ttp80) REVERT: N 106 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5850 (mp0) REVERT: N 134 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6463 (tttt) REVERT: O 24 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.4747 (tpm170) REVERT: O 29 PHE cc_start: 0.6399 (t80) cc_final: 0.6110 (t80) REVERT: O 133 GLU cc_start: 0.3606 (OUTLIER) cc_final: 0.3389 (mp0) REVERT: P 53 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7294 (m) REVERT: P 85 MET cc_start: 0.6685 (mmp) cc_final: 0.6149 (mtt) REVERT: Q 98 GLU cc_start: 0.5104 (pp20) cc_final: 0.4707 (pp20) REVERT: Q 125 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.4963 (tp30) REVERT: Q 127 MET cc_start: 0.4834 (mmp) cc_final: 0.4554 (mmp) REVERT: R 76 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5224 (ptt90) REVERT: R 96 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6937 (ttp) REVERT: R 97 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7638 (tp) REVERT: R 110 ASN cc_start: 0.6150 (OUTLIER) cc_final: 0.5703 (p0) REVERT: S 45 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6690 (mptm) REVERT: S 54 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6105 (tp30) outliers start: 190 outliers final: 102 residues processed: 678 average time/residue: 1.5439 time to fit residues: 1200.7805 Evaluate side-chains 664 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 532 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 60 GLN Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 112 MET Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 43 MET Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 476 HIS Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 20 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 102 GLU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 6.9990 chunk 303 optimal weight: 0.4980 chunk 277 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 267 optimal weight: 0.6980 chunk 279 optimal weight: 10.0000 chunk 294 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN J 101 ASN K 26 ASN K 29 HIS K 383 GLN K 463 ASN K 476 HIS ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27522 Z= 0.224 Angle : 0.718 14.657 37298 Z= 0.348 Chirality : 0.042 0.299 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.172 88.808 4557 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.00 % Favored : 96.79 % Rotamer: Outliers : 6.06 % Allowed : 29.61 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.76 (0.15), residues: 3300 helix: 1.12 (0.10), residues: 2591 sheet: 0.39 (1.36), residues: 19 loop : -1.76 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.007 0.001 HIS K 29 PHE 0.016 0.002 PHE F 31 TYR 0.034 0.002 TYR L 152 ARG 0.011 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 553 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.5571 (t80) cc_final: 0.5019 (t80) REVERT: A 110 LYS cc_start: 0.7263 (mmmt) cc_final: 0.6967 (mmmt) REVERT: B 2 GLN cc_start: 0.5842 (mm-40) cc_final: 0.5519 (mm-40) REVERT: B 17 LYS cc_start: 0.5826 (pttp) cc_final: 0.5616 (pttp) REVERT: B 77 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7495 (mtp180) REVERT: B 151 TYR cc_start: 0.5074 (t80) cc_final: 0.4494 (t80) REVERT: B 152 TYR cc_start: 0.6527 (m-80) cc_final: 0.6183 (m-80) REVERT: C 53 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5821 (mtm-85) REVERT: C 98 ASP cc_start: 0.6697 (p0) cc_final: 0.6391 (p0) REVERT: C 102 ARG cc_start: 0.5918 (mtm110) cc_final: 0.5305 (mtm180) REVERT: C 146 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6270 (mt) REVERT: D 1 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5785 (pmt) REVERT: D 58 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6853 (ptmt) REVERT: E 38 ARG cc_start: 0.5663 (ttp80) cc_final: 0.5351 (ttp80) REVERT: E 60 GLU cc_start: 0.5851 (mp0) cc_final: 0.5621 (mp0) REVERT: E 93 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6513 (mt) REVERT: E 121 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.5235 (ppp80) REVERT: F 42 MET cc_start: 0.5162 (mtp) cc_final: 0.4745 (tpp) REVERT: F 58 LYS cc_start: 0.6731 (ptmt) cc_final: 0.6405 (ptpt) REVERT: G 16 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6627 (ptm160) REVERT: G 73 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5689 (ppp80) REVERT: G 79 GLN cc_start: 0.5923 (OUTLIER) cc_final: 0.5624 (tp40) REVERT: G 98 GLU cc_start: 0.6219 (pm20) cc_final: 0.5675 (pm20) REVERT: G 123 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7399 (mm) REVERT: G 125 GLU cc_start: 0.5820 (tm-30) cc_final: 0.5531 (pt0) REVERT: G 127 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5555 (mpm) REVERT: G 135 MET cc_start: 0.6040 (mmp) cc_final: 0.5505 (mmp) REVERT: G 150 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.4876 (t80) REVERT: H 1 MET cc_start: 0.5750 (OUTLIER) cc_final: 0.5138 (ttm) REVERT: H 100 ASP cc_start: 0.5933 (t70) cc_final: 0.5434 (t0) REVERT: H 147 LYS cc_start: 0.5350 (OUTLIER) cc_final: 0.4584 (mmmm) REVERT: I 89 ILE cc_start: 0.7302 (mt) cc_final: 0.6931 (tt) REVERT: J 21 ARG cc_start: 0.2077 (OUTLIER) cc_final: 0.0554 (tpt170) REVERT: J 24 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5416 (mt) REVERT: J 29 SER cc_start: 0.7823 (t) cc_final: 0.7608 (m) REVERT: J 39 LYS cc_start: 0.7151 (mtmt) cc_final: 0.6747 (mtmm) REVERT: J 58 LYS cc_start: 0.5976 (ttmt) cc_final: 0.5669 (mtmt) REVERT: J 78 ARG cc_start: 0.6866 (mmm-85) cc_final: 0.6472 (mtm-85) REVERT: K 272 SER cc_start: 0.6513 (p) cc_final: 0.6196 (p) REVERT: K 626 TYR cc_start: 0.5772 (m-80) cc_final: 0.4831 (m-80) REVERT: K 691 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5776 (pp20) REVERT: K 692 TYR cc_start: 0.6055 (t80) cc_final: 0.5838 (t80) REVERT: L 76 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6320 (ptm-80) REVERT: L 96 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6466 (ttm) REVERT: M 53 ASN cc_start: 0.5496 (m-40) cc_final: 0.5241 (m-40) REVERT: M 73 ARG cc_start: 0.6577 (tmm160) cc_final: 0.6227 (tmm160) REVERT: M 98 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5413 (pm20) REVERT: M 110 LYS cc_start: 0.6397 (mmmt) cc_final: 0.6193 (tppp) REVERT: N 1 MET cc_start: 0.4712 (tmt) cc_final: 0.3973 (ptm) REVERT: N 8 LEU cc_start: 0.6465 (mt) cc_final: 0.6223 (mp) REVERT: N 105 ASP cc_start: 0.6412 (m-30) cc_final: 0.6176 (m-30) REVERT: N 106 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5908 (mp0) REVERT: N 134 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6504 (tttt) REVERT: N 135 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6776 (mm-30) REVERT: O 24 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.4734 (tpm170) REVERT: O 29 PHE cc_start: 0.6458 (t80) cc_final: 0.6124 (t80) REVERT: O 48 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4828 (mp0) REVERT: P 53 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7237 (m) REVERT: P 85 MET cc_start: 0.6598 (mmp) cc_final: 0.6096 (mtt) REVERT: Q 98 GLU cc_start: 0.5065 (pp20) cc_final: 0.4674 (pp20) REVERT: Q 125 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.4892 (tp30) REVERT: Q 127 MET cc_start: 0.4754 (mmp) cc_final: 0.4498 (mmp) REVERT: R 76 ARG cc_start: 0.5880 (OUTLIER) cc_final: 0.5160 (ptt90) REVERT: R 96 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6932 (ttp) REVERT: R 110 ASN cc_start: 0.6183 (OUTLIER) cc_final: 0.5742 (p0) REVERT: S 45 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6533 (mptm) REVERT: S 54 GLU cc_start: 0.6438 (mm-30) cc_final: 0.5995 (tp30) outliers start: 169 outliers final: 104 residues processed: 660 average time/residue: 1.4896 time to fit residues: 1129.4241 Evaluate side-chains 661 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 528 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 155 GLN Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 628 ASP Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 688 THR Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 133 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 20 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 17 ARG Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 327 optimal weight: 0.9980 chunk 301 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 79 GLN H 117 ASN H 131 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 26 ASN K 29 HIS K 212 GLN K 215 GLN K 463 ASN K 476 HIS ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27522 Z= 0.219 Angle : 0.713 12.419 37298 Z= 0.348 Chirality : 0.042 0.301 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.179 89.454 4557 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.00 % Favored : 96.82 % Rotamer: Outliers : 5.20 % Allowed : 30.90 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.84 (0.15), residues: 3300 helix: 1.17 (0.10), residues: 2593 sheet: 0.33 (1.36), residues: 19 loop : -1.69 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.007 0.001 HIS K 29 PHE 0.020 0.002 PHE F 31 TYR 0.033 0.002 TYR L 152 ARG 0.012 0.001 ARG K 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6600 Ramachandran restraints generated. 3300 Oldfield, 0 Emsley, 3300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 537 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.6974 (ptt90) cc_final: 0.6284 (ptt90) REVERT: A 26 PHE cc_start: 0.5785 (t80) cc_final: 0.5143 (t80) REVERT: A 110 LYS cc_start: 0.7252 (mmmt) cc_final: 0.6959 (mmmt) REVERT: B 2 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5509 (mm-40) REVERT: B 8 LEU cc_start: 0.6878 (mt) cc_final: 0.6664 (mp) REVERT: B 17 LYS cc_start: 0.5851 (pttp) cc_final: 0.5593 (pttp) REVERT: B 77 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7505 (mtp180) REVERT: B 151 TYR cc_start: 0.5084 (t80) cc_final: 0.4552 (t80) REVERT: B 152 TYR cc_start: 0.6482 (m-80) cc_final: 0.6134 (m-80) REVERT: C 31 LYS cc_start: 0.6360 (mtmm) cc_final: 0.5996 (mppt) REVERT: C 53 ARG cc_start: 0.6089 (OUTLIER) cc_final: 0.5820 (mtm-85) REVERT: C 98 ASP cc_start: 0.6656 (p0) cc_final: 0.6364 (p0) REVERT: C 102 ARG cc_start: 0.5858 (mtm110) cc_final: 0.5254 (mtm180) REVERT: C 146 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6311 (mt) REVERT: D 1 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.5804 (pmt) REVERT: D 58 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6839 (ptmt) REVERT: E 38 ARG cc_start: 0.5605 (ttp80) cc_final: 0.5181 (ttp-170) REVERT: E 60 GLU cc_start: 0.5818 (mp0) cc_final: 0.5587 (mp0) REVERT: E 93 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6498 (mt) REVERT: E 121 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5229 (ppp80) REVERT: F 17 LYS cc_start: 0.6312 (pptt) cc_final: 0.6085 (pptt) REVERT: F 42 MET cc_start: 0.5087 (mtp) cc_final: 0.4632 (tpp) REVERT: F 54 LYS cc_start: 0.6381 (OUTLIER) cc_final: 0.6117 (mtpp) REVERT: F 58 LYS cc_start: 0.6764 (ptmt) cc_final: 0.6411 (ptpt) REVERT: G 16 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.6615 (ptm160) REVERT: G 73 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5656 (ppp80) REVERT: G 98 GLU cc_start: 0.6237 (pm20) cc_final: 0.5693 (pm20) REVERT: G 123 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7461 (mm) REVERT: G 127 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.5473 (mpm) REVERT: G 135 MET cc_start: 0.5986 (mmp) cc_final: 0.5486 (mmp) REVERT: G 150 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.4854 (t80) REVERT: H 1 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5164 (ttm) REVERT: H 100 ASP cc_start: 0.5944 (t70) cc_final: 0.5410 (t0) REVERT: H 147 LYS cc_start: 0.5361 (OUTLIER) cc_final: 0.4602 (mmmm) REVERT: I 89 ILE cc_start: 0.7293 (mt) cc_final: 0.6962 (tt) REVERT: I 158 MET cc_start: 0.6211 (tpt) cc_final: 0.5835 (tpt) REVERT: J 21 ARG cc_start: 0.2085 (OUTLIER) cc_final: 0.1011 (tpt170) REVERT: J 29 SER cc_start: 0.7813 (t) cc_final: 0.7596 (p) REVERT: J 39 LYS cc_start: 0.7097 (mtmt) cc_final: 0.6741 (mtmm) REVERT: J 58 LYS cc_start: 0.5971 (ttmt) cc_final: 0.5654 (mtmt) REVERT: K 272 SER cc_start: 0.6429 (p) cc_final: 0.6101 (p) REVERT: K 626 TYR cc_start: 0.5903 (m-80) cc_final: 0.4854 (m-80) REVERT: K 691 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5839 (pp20) REVERT: K 692 TYR cc_start: 0.6035 (t80) cc_final: 0.5779 (t80) REVERT: L 76 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6327 (ptm-80) REVERT: L 96 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6456 (ttm) REVERT: M 53 ASN cc_start: 0.5496 (m-40) cc_final: 0.5202 (m-40) REVERT: M 73 ARG cc_start: 0.6554 (tmm160) cc_final: 0.6298 (tmm160) REVERT: M 110 LYS cc_start: 0.6349 (mmmt) cc_final: 0.6107 (tppp) REVERT: N 8 LEU cc_start: 0.6414 (mt) cc_final: 0.6176 (mp) REVERT: N 76 ARG cc_start: 0.6017 (ttp80) cc_final: 0.5815 (ttp80) REVERT: N 106 GLU cc_start: 0.6124 (mm-30) cc_final: 0.5909 (mp0) REVERT: N 134 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6482 (tttt) REVERT: N 135 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6759 (mm-30) REVERT: N 140 MET cc_start: 0.4081 (pmt) cc_final: 0.3419 (pmm) REVERT: O 24 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.4743 (tpm170) REVERT: O 29 PHE cc_start: 0.6459 (t80) cc_final: 0.6166 (t80) REVERT: O 48 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4859 (mp0) REVERT: O 133 GLU cc_start: 0.3571 (OUTLIER) cc_final: 0.3361 (mp0) REVERT: P 53 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7264 (m) REVERT: P 85 MET cc_start: 0.6617 (mmp) cc_final: 0.6089 (mtt) REVERT: Q 98 GLU cc_start: 0.5043 (pp20) cc_final: 0.4661 (pp20) REVERT: Q 125 GLU cc_start: 0.5411 (OUTLIER) cc_final: 0.4876 (tp30) REVERT: Q 145 GLU cc_start: 0.4273 (mt-10) cc_final: 0.4044 (pt0) REVERT: R 76 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5162 (ptt90) REVERT: R 96 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6911 (ttp) REVERT: R 110 ASN cc_start: 0.6296 (OUTLIER) cc_final: 0.5848 (p0) REVERT: S 45 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6498 (mptm) outliers start: 145 outliers final: 98 residues processed: 636 average time/residue: 1.5241 time to fit residues: 1110.8745 Evaluate side-chains 653 residues out of total 2792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 527 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 165 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain J residue 153 ILE Chi-restraints excluded: chain J residue 155 GLN Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 218 SER Chi-restraints excluded: chain K residue 443 VAL Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 501 HIS Chi-restraints excluded: chain K residue 542 VAL Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 580 GLU Chi-restraints excluded: chain K residue 628 ASP Chi-restraints excluded: chain K residue 655 ASN Chi-restraints excluded: chain K residue 666 ARG Chi-restraints excluded: chain K residue 679 ILE Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain K residue 695 ARG Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 133 MET Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 71 VAL Chi-restraints excluded: chain M residue 92 SER Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 20 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 ARG Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 82 ILE Chi-restraints excluded: chain N residue 134 LYS Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 24 ARG Chi-restraints excluded: chain O residue 48 GLU Chi-restraints excluded: chain O residue 127 MET Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 36 LEU Chi-restraints excluded: chain P residue 50 THR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 65 ILE Chi-restraints excluded: chain P residue 75 CYS Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 125 GLU Chi-restraints excluded: chain Q residue 133 GLU Chi-restraints excluded: chain R residue 42 MET Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 114 GLU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 268 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 79 GLN H 117 ASN ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 71 ASN J 101 ASN K 26 ASN K 29 HIS K 463 ASN ** L 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** N 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.225117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.204791 restraints weight = 31119.825| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 1.55 r_work: 0.4241 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4089 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27522 Z= 0.230 Angle : 0.733 12.617 37298 Z= 0.357 Chirality : 0.042 0.314 4096 Planarity : 0.005 0.060 4812 Dihedral : 9.166 89.325 4556 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer: Outliers : 5.41 % Allowed : 31.08 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 0.80 (0.15), residues: 3300 helix: 1.14 (0.10), residues: 2593 sheet: 0.14 (1.34), residues: 19 loop : -1.70 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 84 HIS 0.007 0.001 HIS K 29 PHE 0.018 0.002 PHE F 31 TYR 0.033 0.002 TYR L 152 ARG 0.012 0.001 ARG K 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14918.34 seconds wall clock time: 262 minutes 19.96 seconds (15739.96 seconds total)