Starting phenix.real_space_refine on Sat Dec 16 13:08:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znj_14803/12_2023/7znj_14803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znj_14803/12_2023/7znj_14803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znj_14803/12_2023/7znj_14803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znj_14803/12_2023/7znj_14803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znj_14803/12_2023/7znj_14803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7znj_14803/12_2023/7znj_14803_updated.pdb" } resolution = 2.4 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= 0.003 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 6 5.21 5 S 156 5.16 5 C 22086 2.51 5 N 5994 2.21 5 O 6798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "a ASP 48": "OD1" <-> "OD2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a GLU 148": "OE1" <-> "OE2" Residue "a TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 227": "OE1" <-> "OE2" Residue "a ASP 266": "OD1" <-> "OD2" Residue "a ASP 335": "OD1" <-> "OD2" Residue "a ASP 342": "OD1" <-> "OD2" Residue "a ASP 385": "OD1" <-> "OD2" Residue "a ASP 401": "OD1" <-> "OD2" Residue "a GLU 402": "OE1" <-> "OE2" Residue "b TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 23": "OE1" <-> "OE2" Residue "b TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 49": "OE1" <-> "OE2" Residue "b TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 68": "OE1" <-> "OE2" Residue "b GLU 72": "OE1" <-> "OE2" Residue "b ASP 73": "OD1" <-> "OD2" Residue "b GLU 89": "OE1" <-> "OE2" Residue "b PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 122": "OE1" <-> "OE2" Residue "c TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 126": "OE1" <-> "OE2" Residue "d ASP 114": "OD1" <-> "OD2" Residue "d ASP 121": "OD1" <-> "OD2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F GLU 322": "OE1" <-> "OE2" Residue "F ASP 342": "OD1" <-> "OD2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F ASP 385": "OD1" <-> "OD2" Residue "F ASP 401": "OD1" <-> "OD2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 23": "OE1" <-> "OE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 147": "OD1" <-> "OD2" Residue "I ASP 119": "OD1" <-> "OD2" Residue "I ASP 140": "OD1" <-> "OD2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f ASP 48": "OD1" <-> "OD2" Residue "f GLU 59": "OE1" <-> "OE2" Residue "f GLU 227": "OE1" <-> "OE2" Residue "f ASP 273": "OD1" <-> "OD2" Residue "f GLU 315": "OE1" <-> "OE2" Residue "f GLU 317": "OE1" <-> "OE2" Residue "f ASP 342": "OD1" <-> "OD2" Residue "f GLU 359": "OE1" <-> "OE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 23": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 65": "OD1" <-> "OD2" Residue "g GLU 68": "OE1" <-> "OE2" Residue "g ASP 73": "OD1" <-> "OD2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 89": "OE1" <-> "OE2" Residue "g PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 109": "OD1" <-> "OD2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h GLU 120": "OE1" <-> "OE2" Residue "h GLU 122": "OE1" <-> "OE2" Residue "h TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 147": "OD1" <-> "OD2" Residue "i ASP 114": "OD1" <-> "OD2" Residue "i ASP 121": "OD1" <-> "OD2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K ASP 35": "OD1" <-> "OD2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 191": "OE1" <-> "OE2" Residue "K TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 315": "OE1" <-> "OE2" Residue "K GLU 322": "OE1" <-> "OE2" Residue "K ASP 335": "OD1" <-> "OD2" Residue "K GLU 402": "OE1" <-> "OE2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 65": "OD1" <-> "OD2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 109": "OD1" <-> "OD2" Residue "L GLU 117": "OE1" <-> "OE2" Residue "M TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "M ASP 147": "OD1" <-> "OD2" Residue "N ASP 114": "OD1" <-> "OD2" Residue "N ASP 119": "OD1" <-> "OD2" Residue "N ASP 158": "OD1" <-> "OD2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ASP 35": "OD1" <-> "OD2" Residue "k ASP 48": "OD1" <-> "OD2" Residue "k GLU 59": "OE1" <-> "OE2" Residue "k ASP 77": "OD1" <-> "OD2" Residue "k TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 227": "OE1" <-> "OE2" Residue "k ASP 235": "OD1" <-> "OD2" Residue "k PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 315": "OE1" <-> "OE2" Residue "k ASP 335": "OD1" <-> "OD2" Residue "k ASP 342": "OD1" <-> "OD2" Residue "k ASP 385": "OD1" <-> "OD2" Residue "l TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 23": "OE1" <-> "OE2" Residue "l TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 65": "OD1" <-> "OD2" Residue "l GLU 68": "OE1" <-> "OE2" Residue "l GLU 89": "OE1" <-> "OE2" Residue "l PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "m GLU 122": "OE1" <-> "OE2" Residue "m TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 126": "OE1" <-> "OE2" Residue "n ASP 114": "OD1" <-> "OD2" Residue "n ASP 121": "OD1" <-> "OD2" Residue "n ASP 140": "OD1" <-> "OD2" Residue "n ASP 158": "OD1" <-> "OD2" Time to flip residues: 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35088 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "B" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "C" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "a" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "b" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "d" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "G" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "f" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "g" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "h" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "i" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "L" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "M" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "N" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "k" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "l" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "m" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "n" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.97, per 1000 atoms: 0.51 Number of scatterers: 35088 At special positions: 0 Unit cell: (176.715, 166.32, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 P 48 15.00 Mg 6 11.99 O 6798 8.00 N 5994 7.00 C 22086 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=0, symmetry=0 Time building additional restraints: 13.55 Conformation dependent library (CDL) restraints added in 6.2 seconds 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 30 sheets defined 33.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.507A pdb=" N TYR A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.940A pdb=" N ILE A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.628A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 189 through 192 No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 198 through 207 removed outlier: 4.181A pdb=" N TYR A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.557A pdb=" N MET A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 261 through 270 removed outlier: 4.026A pdb=" N PHE A 265 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS A 269 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 358 through 367 removed outlier: 3.749A pdb=" N ILE A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'B' and resid 54 through 67 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 116 through 141 removed outlier: 3.519A pdb=" N GLN B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.586A pdb=" N LYS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'a' and resid 40 through 42 No H-bonds generated for 'chain 'a' and resid 40 through 42' Processing helix chain 'a' and resid 47 through 56 Processing helix chain 'a' and resid 65 through 73 removed outlier: 3.989A pdb=" N ILE a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN a 71 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 98 removed outlier: 3.604A pdb=" N PHE a 92 " --> pdb=" O LYS a 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU a 97 " --> pdb=" O SER a 93 " (cutoff:3.500A) Processing helix chain 'a' and resid 116 through 129 Processing helix chain 'a' and resid 146 through 155 Processing helix chain 'a' and resid 164 through 172 Processing helix chain 'a' and resid 189 through 192 No H-bonds generated for 'chain 'a' and resid 189 through 192' Processing helix chain 'a' and resid 198 through 207 removed outlier: 4.168A pdb=" N TYR a 207 " --> pdb=" O ASP a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 223 through 231 removed outlier: 3.623A pdb=" N MET a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN a 230 " --> pdb=" O LEU a 226 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYS a 231 " --> pdb=" O GLU a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 245 No H-bonds generated for 'chain 'a' and resid 243 through 245' Processing helix chain 'a' and resid 264 through 270 removed outlier: 3.555A pdb=" N ASP a 270 " --> pdb=" O ASP a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 272 through 275 No H-bonds generated for 'chain 'a' and resid 272 through 275' Processing helix chain 'a' and resid 287 through 299 Processing helix chain 'a' and resid 313 through 325 Processing helix chain 'a' and resid 335 through 337 No H-bonds generated for 'chain 'a' and resid 335 through 337' Processing helix chain 'a' and resid 358 through 367 removed outlier: 3.752A pdb=" N ILE a 362 " --> pdb=" O ARG a 358 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS a 363 " --> pdb=" O GLU a 359 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG a 367 " --> pdb=" O HIS a 363 " (cutoff:3.500A) Processing helix chain 'a' and resid 386 through 396 Processing helix chain 'b' and resid 54 through 67 Processing helix chain 'b' and resid 69 through 71 No H-bonds generated for 'chain 'b' and resid 69 through 71' Processing helix chain 'b' and resid 107 through 111 Processing helix chain 'b' and resid 116 through 141 removed outlier: 3.524A pdb=" N GLN b 127 " --> pdb=" O TYR b 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 93 Processing helix chain 'c' and resid 124 through 134 Processing helix chain 'd' and resid 119 through 126 Processing helix chain 'd' and resid 156 through 166 Processing helix chain 'F' and resid 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 65 through 73 removed outlier: 3.965A pdb=" N ILE F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.598A pdb=" N PHE F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 129 Processing helix chain 'F' and resid 146 through 155 Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 189 through 192 No H-bonds generated for 'chain 'F' and resid 189 through 192' Processing helix chain 'F' and resid 198 through 207 removed outlier: 4.170A pdb=" N TYR F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 231 removed outlier: 3.589A pdb=" N MET F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN F 230 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 264 through 270 Processing helix chain 'F' and resid 272 through 275 No H-bonds generated for 'chain 'F' and resid 272 through 275' Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.525A pdb=" N ARG F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 358 through 367 removed outlier: 3.804A pdb=" N ILE F 362 " --> pdb=" O ARG F 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 367 " --> pdb=" O HIS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'G' and resid 54 through 67 Processing helix chain 'G' and resid 69 through 71 No H-bonds generated for 'chain 'G' and resid 69 through 71' Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 116 through 141 removed outlier: 3.503A pdb=" N VAL G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN G 127 " --> pdb=" O TYR G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 93 Processing helix chain 'H' and resid 124 through 134 Processing helix chain 'I' and resid 119 through 126 Processing helix chain 'I' and resid 156 through 166 Processing helix chain 'f' and resid 40 through 42 No H-bonds generated for 'chain 'f' and resid 40 through 42' Processing helix chain 'f' and resid 47 through 56 Processing helix chain 'f' and resid 65 through 73 removed outlier: 3.968A pdb=" N ILE f 69 " --> pdb=" O GLN f 65 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS f 70 " --> pdb=" O GLN f 66 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN f 71 " --> pdb=" O ARG f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 98 removed outlier: 3.640A pdb=" N PHE f 92 " --> pdb=" O LYS f 88 " (cutoff:3.500A) Processing helix chain 'f' and resid 116 through 129 Processing helix chain 'f' and resid 146 through 155 Processing helix chain 'f' and resid 164 through 172 Processing helix chain 'f' and resid 189 through 192 No H-bonds generated for 'chain 'f' and resid 189 through 192' Processing helix chain 'f' and resid 198 through 207 removed outlier: 4.242A pdb=" N TYR f 207 " --> pdb=" O ASP f 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 223 through 231 removed outlier: 3.514A pdb=" N MET f 228 " --> pdb=" O GLU f 224 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR f 229 " --> pdb=" O ILE f 225 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN f 230 " --> pdb=" O LEU f 226 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS f 231 " --> pdb=" O GLU f 227 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 245 No H-bonds generated for 'chain 'f' and resid 243 through 245' Processing helix chain 'f' and resid 264 through 270 Processing helix chain 'f' and resid 272 through 276 Processing helix chain 'f' and resid 287 through 299 Processing helix chain 'f' and resid 313 through 324 Processing helix chain 'f' and resid 335 through 337 No H-bonds generated for 'chain 'f' and resid 335 through 337' Processing helix chain 'f' and resid 358 through 367 removed outlier: 3.820A pdb=" N ILE f 362 " --> pdb=" O ARG f 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS f 363 " --> pdb=" O GLU f 359 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG f 367 " --> pdb=" O HIS f 363 " (cutoff:3.500A) Processing helix chain 'f' and resid 386 through 395 Processing helix chain 'g' and resid 54 through 67 Processing helix chain 'g' and resid 69 through 71 No H-bonds generated for 'chain 'g' and resid 69 through 71' Processing helix chain 'g' and resid 107 through 111 Processing helix chain 'g' and resid 116 through 141 removed outlier: 3.536A pdb=" N GLN g 127 " --> pdb=" O TYR g 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 86 through 93 Processing helix chain 'h' and resid 124 through 134 Processing helix chain 'i' and resid 119 through 126 Processing helix chain 'i' and resid 156 through 166 Processing helix chain 'K' and resid 47 through 56 Processing helix chain 'K' and resid 65 through 73 removed outlier: 3.974A pdb=" N ILE K 69 " --> pdb=" O GLN K 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS K 70 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 98 removed outlier: 3.604A pdb=" N PHE K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 129 Processing helix chain 'K' and resid 146 through 155 Processing helix chain 'K' and resid 164 through 172 Processing helix chain 'K' and resid 189 through 192 No H-bonds generated for 'chain 'K' and resid 189 through 192' Processing helix chain 'K' and resid 198 through 207 removed outlier: 4.187A pdb=" N TYR K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 231 removed outlier: 3.720A pdb=" N MET K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR K 229 " --> pdb=" O ILE K 225 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 245 No H-bonds generated for 'chain 'K' and resid 243 through 245' Processing helix chain 'K' and resid 264 through 270 Processing helix chain 'K' and resid 272 through 275 No H-bonds generated for 'chain 'K' and resid 272 through 275' Processing helix chain 'K' and resid 287 through 299 Processing helix chain 'K' and resid 313 through 324 Processing helix chain 'K' and resid 335 through 337 No H-bonds generated for 'chain 'K' and resid 335 through 337' Processing helix chain 'K' and resid 358 through 367 removed outlier: 3.788A pdb=" N ILE K 362 " --> pdb=" O ARG K 358 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS K 363 " --> pdb=" O GLU K 359 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG K 367 " --> pdb=" O HIS K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 395 Processing helix chain 'L' and resid 54 through 67 Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 116 through 141 removed outlier: 3.527A pdb=" N GLN L 127 " --> pdb=" O TYR L 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 124 through 134 Processing helix chain 'N' and resid 119 through 126 Processing helix chain 'N' and resid 156 through 166 Processing helix chain 'k' and resid 40 through 42 No H-bonds generated for 'chain 'k' and resid 40 through 42' Processing helix chain 'k' and resid 47 through 56 Processing helix chain 'k' and resid 65 through 73 removed outlier: 3.983A pdb=" N ILE k 69 " --> pdb=" O GLN k 65 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS k 70 " --> pdb=" O GLN k 66 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN k 71 " --> pdb=" O ARG k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 88 through 98 removed outlier: 3.609A pdb=" N PHE k 92 " --> pdb=" O LYS k 88 " (cutoff:3.500A) Processing helix chain 'k' and resid 116 through 129 Processing helix chain 'k' and resid 146 through 155 Processing helix chain 'k' and resid 164 through 172 Processing helix chain 'k' and resid 189 through 192 No H-bonds generated for 'chain 'k' and resid 189 through 192' Processing helix chain 'k' and resid 198 through 207 removed outlier: 4.081A pdb=" N TYR k 207 " --> pdb=" O ASP k 203 " (cutoff:3.500A) Processing helix chain 'k' and resid 223 through 231 removed outlier: 3.684A pdb=" N MET k 228 " --> pdb=" O GLU k 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR k 229 " --> pdb=" O ILE k 225 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN k 230 " --> pdb=" O LEU k 226 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS k 231 " --> pdb=" O GLU k 227 " (cutoff:3.500A) Processing helix chain 'k' and resid 261 through 270 removed outlier: 3.539A pdb=" N LYS k 264 " --> pdb=" O GLU k 261 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE k 265 " --> pdb=" O GLU k 262 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N CYS k 269 " --> pdb=" O ASP k 266 " (cutoff:3.500A) Processing helix chain 'k' and resid 272 through 275 No H-bonds generated for 'chain 'k' and resid 272 through 275' Processing helix chain 'k' and resid 287 through 299 Processing helix chain 'k' and resid 313 through 325 Processing helix chain 'k' and resid 358 through 367 removed outlier: 3.735A pdb=" N ILE k 362 " --> pdb=" O ARG k 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS k 363 " --> pdb=" O GLU k 359 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG k 367 " --> pdb=" O HIS k 363 " (cutoff:3.500A) Processing helix chain 'k' and resid 386 through 395 Processing helix chain 'l' and resid 54 through 67 Processing helix chain 'l' and resid 69 through 71 No H-bonds generated for 'chain 'l' and resid 69 through 71' Processing helix chain 'l' and resid 107 through 111 Processing helix chain 'l' and resid 116 through 141 removed outlier: 3.558A pdb=" N GLN l 127 " --> pdb=" O TYR l 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 93 Processing helix chain 'm' and resid 124 through 134 Processing helix chain 'n' and resid 119 through 126 Processing helix chain 'n' and resid 156 through 166 Processing sheet with id= A, first strand: chain 'A' and resid 237 through 239 Processing sheet with id= B, first strand: chain 'A' and resid 251 through 257 removed outlier: 6.681A pdb=" N GLY A 375 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE A 254 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA A 377 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL A 256 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN A 379 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN A 279 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE A 349 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 281 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 351 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 283 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.619A pdb=" N GLY B 18 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 95 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 145 through 148 removed outlier: 4.217A pdb=" N ASN C 101 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 177 through 180 removed outlier: 3.982A pdb=" N GLY D 106 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'a' and resid 237 through 239 removed outlier: 3.741A pdb=" N THR a 163 " --> pdb=" O CYS a 140 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'a' and resid 251 through 257 removed outlier: 6.639A pdb=" N GLY a 375 " --> pdb=" O LYS a 252 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE a 254 " --> pdb=" O GLY a 375 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA a 377 " --> pdb=" O PHE a 254 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL a 256 " --> pdb=" O ALA a 377 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN a 379 " --> pdb=" O VAL a 256 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN a 279 " --> pdb=" O SER a 347 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE a 349 " --> pdb=" O GLN a 279 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL a 281 " --> pdb=" O ILE a 349 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASN a 351 " --> pdb=" O VAL a 281 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE a 283 " --> pdb=" O ASN a 351 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER a 305 " --> pdb=" O ILE a 332 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'b' and resid 46 through 51 removed outlier: 3.506A pdb=" N GLY b 18 " --> pdb=" O GLY b 15 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU b 95 " --> pdb=" O ILE b 92 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'c' and resid 145 through 148 removed outlier: 4.093A pdb=" N ASN c 101 " --> pdb=" O GLU c 120 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 177 through 180 removed outlier: 4.010A pdb=" N GLY d 106 " --> pdb=" O PHE d 153 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 237 through 239 removed outlier: 3.705A pdb=" N THR F 163 " --> pdb=" O CYS F 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 251 through 257 removed outlier: 6.625A pdb=" N GLY F 375 " --> pdb=" O LYS F 252 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N PHE F 254 " --> pdb=" O GLY F 375 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA F 377 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL F 256 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN F 379 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN F 279 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE F 349 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL F 281 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASN F 351 " --> pdb=" O VAL F 281 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE F 283 " --> pdb=" O ASN F 351 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N SER F 305 " --> pdb=" O ILE F 332 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 46 through 51 removed outlier: 3.530A pdb=" N GLU G 95 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 145 through 148 removed outlier: 4.102A pdb=" N ASN H 101 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 177 through 180 removed outlier: 4.001A pdb=" N GLY I 106 " --> pdb=" O PHE I 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 134 " --> pdb=" O HIS I 152 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'f' and resid 237 through 239 Processing sheet with id= Q, first strand: chain 'f' and resid 251 through 257 removed outlier: 6.693A pdb=" N GLY f 375 " --> pdb=" O LYS f 252 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE f 254 " --> pdb=" O GLY f 375 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA f 377 " --> pdb=" O PHE f 254 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL f 256 " --> pdb=" O ALA f 377 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN f 379 " --> pdb=" O VAL f 256 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLN f 279 " --> pdb=" O SER f 347 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE f 349 " --> pdb=" O GLN f 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL f 281 " --> pdb=" O ILE f 349 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASN f 351 " --> pdb=" O VAL f 281 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE f 283 " --> pdb=" O ASN f 351 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER f 305 " --> pdb=" O ILE f 332 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'g' and resid 46 through 51 removed outlier: 3.612A pdb=" N GLY g 18 " --> pdb=" O GLY g 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU g 95 " --> pdb=" O ILE g 92 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'h' and resid 145 through 148 removed outlier: 4.216A pdb=" N ASN h 101 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'i' and resid 177 through 179 removed outlier: 3.874A pdb=" N GLY i 106 " --> pdb=" O PHE i 153 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS i 134 " --> pdb=" O HIS i 152 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 237 through 239 removed outlier: 3.762A pdb=" N THR K 163 " --> pdb=" O CYS K 140 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 251 through 257 removed outlier: 6.680A pdb=" N GLY K 375 " --> pdb=" O LYS K 252 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE K 254 " --> pdb=" O GLY K 375 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA K 377 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL K 256 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASN K 379 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN K 279 " --> pdb=" O SER K 347 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE K 349 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL K 281 " --> pdb=" O ILE K 349 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN K 351 " --> pdb=" O VAL K 281 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE K 283 " --> pdb=" O ASN K 351 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N SER K 305 " --> pdb=" O ILE K 332 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 46 through 51 removed outlier: 3.522A pdb=" N GLY L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 95 " --> pdb=" O ILE L 92 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 145 through 148 removed outlier: 4.100A pdb=" N ASN M 101 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 177 through 180 removed outlier: 4.132A pdb=" N GLY N 106 " --> pdb=" O PHE N 153 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS N 134 " --> pdb=" O HIS N 152 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'k' and resid 237 through 239 removed outlier: 3.739A pdb=" N THR k 163 " --> pdb=" O CYS k 140 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'k' and resid 251 through 257 removed outlier: 6.675A pdb=" N GLY k 375 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE k 254 " --> pdb=" O GLY k 375 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA k 377 " --> pdb=" O PHE k 254 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL k 256 " --> pdb=" O ALA k 377 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN k 379 " --> pdb=" O VAL k 256 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN k 279 " --> pdb=" O SER k 347 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE k 349 " --> pdb=" O GLN k 279 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL k 281 " --> pdb=" O ILE k 349 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASN k 351 " --> pdb=" O VAL k 281 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE k 283 " --> pdb=" O ASN k 351 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER k 305 " --> pdb=" O ILE k 332 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'l' and resid 46 through 51 removed outlier: 3.522A pdb=" N GLY l 18 " --> pdb=" O GLY l 15 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'm' and resid 145 through 148 removed outlier: 4.141A pdb=" N ASN m 101 " --> pdb=" O GLU m 120 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'n' and resid 177 through 180 removed outlier: 4.066A pdb=" N GLY n 106 " --> pdb=" O PHE n 153 " (cutoff:3.500A) 1294 hydrogen bonds defined for protein. 3723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.82 Time building geometry restraints manager: 14.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11485 1.34 - 1.46: 8175 1.46 - 1.59: 15811 1.59 - 1.71: 73 1.71 - 1.83: 270 Bond restraints: 35814 Sorted by residual: bond pdb=" O3A ANP a 502 " pdb=" PB ANP a 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP F 502 " pdb=" PB ANP F 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP f 502 " pdb=" PB ANP f 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" O3A ANP k 502 " pdb=" PB ANP k 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 35809 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.87: 836 105.87 - 113.70: 19629 113.70 - 121.53: 19479 121.53 - 129.37: 8375 129.37 - 137.20: 203 Bond angle restraints: 48522 Sorted by residual: angle pdb=" CB LYS D 161 " pdb=" CG LYS D 161 " pdb=" CD LYS D 161 " ideal model delta sigma weight residual 111.30 125.70 -14.40 2.30e+00 1.89e-01 3.92e+01 angle pdb=" C PHE f 58 " pdb=" N GLU f 59 " pdb=" CA GLU f 59 " ideal model delta sigma weight residual 121.54 133.05 -11.51 1.91e+00 2.74e-01 3.63e+01 angle pdb=" CA LEU D 91 " pdb=" CB LEU D 91 " pdb=" CG LEU D 91 " ideal model delta sigma weight residual 116.30 137.20 -20.90 3.50e+00 8.16e-02 3.56e+01 angle pdb=" C PHE A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE F 58 " pdb=" N GLU F 59 " pdb=" CA GLU F 59 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 ... (remaining 48517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 18893 17.70 - 35.39: 1871 35.39 - 53.09: 628 53.09 - 70.78: 184 70.78 - 88.48: 96 Dihedral angle restraints: 21672 sinusoidal: 9408 harmonic: 12264 Sorted by residual: dihedral pdb=" CA TRP i 87 " pdb=" C TRP i 87 " pdb=" N GLN i 88 " pdb=" CA GLN i 88 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP n 87 " pdb=" C TRP n 87 " pdb=" N GLN n 88 " pdb=" CA GLN n 88 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TRP N 87 " pdb=" C TRP N 87 " pdb=" N GLN N 88 " pdb=" CA GLN N 88 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 21669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4153 0.051 - 0.102: 935 0.102 - 0.152: 268 0.152 - 0.203: 8 0.203 - 0.254: 6 Chirality restraints: 5370 Sorted by residual: chirality pdb=" C3' ANP F 502 " pdb=" C2' ANP F 502 " pdb=" C4' ANP F 502 " pdb=" O3' ANP F 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' ANP a 502 " pdb=" C2' ANP a 502 " pdb=" C4' ANP a 502 " pdb=" O3' ANP a 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C3' ANP A 502 " pdb=" C2' ANP A 502 " pdb=" C4' ANP A 502 " pdb=" O3' ANP A 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.60 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5367 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE k 265 " 0.027 2.00e-02 2.50e+03 3.50e-02 2.14e+01 pdb=" CG PHE k 265 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE k 265 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE k 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE k 265 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE k 265 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE k 265 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 91 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C LEU I 91 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU I 91 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE I 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 58 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C PHE A 58 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A 58 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.014 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 376 2.65 - 3.22: 28883 3.22 - 3.78: 53707 3.78 - 4.34: 81077 4.34 - 4.90: 126151 Nonbonded interactions: 290194 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O3G ANP A 502 " model vdw 2.092 2.170 nonbonded pdb="MG MG f 501 " pdb=" O3G ANP f 502 " model vdw 2.098 2.170 nonbonded pdb="MG MG k 501 " pdb=" O3G ANP k 502 " model vdw 2.108 2.170 nonbonded pdb="MG MG K 501 " pdb=" O2B ANP K 502 " model vdw 2.133 2.170 nonbonded pdb="MG MG a 501 " pdb=" O2B ANP a 502 " model vdw 2.139 2.170 ... (remaining 290189 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 'F' selection = chain 'K' selection = chain 'a' selection = chain 'f' selection = chain 'k' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' selection = chain 'b' selection = chain 'g' selection = chain 'l' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'c' selection = chain 'h' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' selection = chain 'd' selection = chain 'i' selection = chain 'n' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'e' selection = chain 'j' selection = chain 'o' } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 9.090 Check model and map are aligned: 0.550 Set scattering table: 0.320 Process input model: 89.240 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.004 0.146 35814 Z= 0.298 Angle : 0.824 20.896 48522 Z= 0.432 Chirality : 0.047 0.254 5370 Planarity : 0.005 0.084 6150 Dihedral : 17.518 88.479 13788 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.83 % Allowed : 17.42 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4182 helix: -3.13 (0.07), residues: 1536 sheet: 1.28 (0.16), residues: 912 loop : 0.16 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP k 337 HIS 0.009 0.001 HIS i 89 PHE 0.080 0.002 PHE k 265 TYR 0.034 0.002 TYR a 155 ARG 0.020 0.001 ARG a 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 625 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 7 residues processed: 641 average time/residue: 1.7643 time to fit residues: 1323.8310 Evaluate side-chains 541 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 534 time to evaluate : 4.114 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.3744 time to fit residues: 6.2843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 329 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 381 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS B 42 ASN B 140 HIS C 128 GLN D 123 GLN ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 351 ASN b 140 HIS c 101 ASN c 128 GLN d 179 GLN G 96 HIS G 140 HIS H 101 ASN H 128 GLN I 179 GLN g 42 ASN g 112 GLN g 127 GLN g 140 HIS h 128 GLN i 152 HIS i 179 GLN L 42 ASN L 86 GLN L 111 ASN L 112 GLN L 140 HIS M 128 GLN N 177 ASN N 179 GLN ** k 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 308 HIS k 351 ASN l 42 ASN l 96 HIS l 140 HIS n 179 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 35814 Z= 0.311 Angle : 0.728 15.373 48522 Z= 0.378 Chirality : 0.049 0.172 5370 Planarity : 0.006 0.062 6150 Dihedral : 9.900 61.889 5280 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 4.04 % Allowed : 14.89 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 4182 helix: -0.86 (0.11), residues: 1542 sheet: 1.51 (0.16), residues: 936 loop : 0.13 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP k 292 HIS 0.007 0.002 HIS i 89 PHE 0.031 0.003 PHE K 92 TYR 0.020 0.003 TYR k 371 ARG 0.007 0.001 ARG K 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 543 time to evaluate : 4.126 Fit side-chains outliers start: 150 outliers final: 56 residues processed: 627 average time/residue: 1.7409 time to fit residues: 1280.0872 Evaluate side-chains 563 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 507 time to evaluate : 3.861 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 33 residues processed: 23 average time/residue: 1.3520 time to fit residues: 43.8351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 317 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 382 optimal weight: 7.9990 chunk 412 optimal weight: 10.0000 chunk 340 optimal weight: 0.2980 chunk 378 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN C 128 GLN D 179 GLN ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN b 111 ASN c 101 ASN c 128 GLN d 179 GLN G 42 ASN H 101 ASN I 179 GLN f 356 ASN g 42 ASN g 111 ASN h 103 HIS h 128 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN L 111 ASN L 112 GLN N 123 GLN ** k 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN m 103 HIS n 123 GLN n 179 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35814 Z= 0.229 Angle : 0.630 14.943 48522 Z= 0.328 Chirality : 0.046 0.149 5370 Planarity : 0.005 0.046 6150 Dihedral : 9.057 58.924 5280 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.74 % Allowed : 14.65 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4182 helix: 0.08 (0.12), residues: 1542 sheet: 1.53 (0.16), residues: 936 loop : 0.19 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 337 HIS 0.007 0.001 HIS i 89 PHE 0.025 0.002 PHE k 92 TYR 0.026 0.002 TYR K 155 ARG 0.006 0.001 ARG f 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 553 time to evaluate : 4.077 Fit side-chains outliers start: 139 outliers final: 66 residues processed: 621 average time/residue: 1.7996 time to fit residues: 1309.3873 Evaluate side-chains 595 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 529 time to evaluate : 4.471 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 38 residues processed: 30 average time/residue: 1.1732 time to fit residues: 50.5566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 9.9990 chunk 287 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 383 optimal weight: 8.9990 chunk 405 optimal weight: 0.0000 chunk 200 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 96 HIS B 111 ASN C 103 HIS C 128 GLN D 177 ASN D 179 GLN a 200 GLN b 42 ASN b 112 GLN c 101 ASN c 103 HIS d 179 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN g 111 ASN g 127 GLN h 128 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN K 200 GLN L 111 ASN L 112 GLN N 123 GLN k 200 GLN ** k 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 ASN m 103 HIS n 123 GLN n 179 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35814 Z= 0.288 Angle : 0.686 15.736 48522 Z= 0.358 Chirality : 0.048 0.159 5370 Planarity : 0.005 0.054 6150 Dihedral : 9.852 63.511 5280 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.82 % Allowed : 14.86 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 4182 helix: 0.34 (0.13), residues: 1530 sheet: 1.46 (0.16), residues: 906 loop : 0.04 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP f 337 HIS 0.008 0.002 HIS K 308 PHE 0.023 0.002 PHE k 92 TYR 0.024 0.003 TYR K 155 ARG 0.005 0.001 ARG k 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 548 time to evaluate : 3.811 Fit side-chains revert: symmetry clash outliers start: 142 outliers final: 78 residues processed: 627 average time/residue: 1.5572 time to fit residues: 1143.5018 Evaluate side-chains 608 residues out of total 3720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 530 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 45 residues processed: 34 average time/residue: 0.8781 time to fit residues: 40.3187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 346 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 207 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: